 Assalamu alaikum and good morning everyone. Welcome to the first session of the second day of the STEM education training program funded by a British Council. Let's start the session with the name of Allah Almighty. Ladies and gentlemen, today we have with us Dr. Muhammad Tariq Parvez. He has been serving Warsaw University of Pakistan since 2005. Currently he is working in the capacity of associate professor and chairman department of bioinformatics and computational biology. He is co-founder of the department of bioinformatics and computation biology and department of biology department of biotechnology department of molecular biology mobile and smart labs. His work comprises construction of genome assembly, whole genome, whole exam data analysis machine learning in prognosis and predicting disease algorithms and database designing and development. He has more than 50 publications in national and international journals and developed multiple bioinformatics databases and tools. He will deliver his talk on genomic variant discovery, interpretations and prioritization using bioinformatics. Welcome sir, please proceed for your presentation. Assalamu alaikum. As you are told that my talk will be on genetic variant analysis using bioinformatics tools. Actually, there was demand from my biofaculty staff for two and three years that we should be trained on bioinformatics tools, SNP analysis, genetic variant analysis, or to make analysis and other bioinformatics analysis techniques. Today I will tell you three main research domains in SNP analysis. SNP analysis works towards after having variants or SNPs as a result of whole exam data analysis or whole genome data analysis. This is a task that you have to do after having variants. You have to interpret those variants. You have to do prioritization. So this is a full-fledged research work, SNP analysis. And then comparison of pathogenicity prediction tools. The tools who predict the impact of SNPs. You can work on their comparison. Some work has been done, some work has been done, even I have two students working on them. Then after that whole exome data analysis or whole genome data analysis. Let's start from whole exome data analysis. These are some problems when you work on, generally if I say on bioinformatics data analysis. Firstly, there is a lack of bioinformatics proper setup. In this, you require high performance computing tools. Earlier I had a workshop on high performance computer clustered designing and building. If you talk about supercomputer, as I told you before, supercomputer is not a standalone computer, it is not a single computer. It is actually a network or collection of several high performance computing machines. So all over the world, especially in Pakistan, this is a problem that we don't have a proper setup. After that, then there is a lack of expertise. You will get very few experts. You have data, but you don't have any expertise or you don't have any person that you can help in this. Then there is a lack of workflow or pipeline. You may have listened about the workflow or bioinformatics pipelines. What are the workflow or pipeline? You must have done some work on bioinformatics nurses, like if I say about alignment generation. After that you must have made a phylogenetic tree. After that you may have worked on some other bioinformatics task. There is a long list of bioinformatics tasks. It happens that you take an output of one tool, then you install another tool, then you install the third tool. Manually you would have to give input to all tools and then save output. In this case, you are working on computing tools separately. There is no system in which you give one input and select three or four options simultaneously. You can do it later, but you don't have to give input or output or save again. In that case, when you go to major department stores, shopping centers, you purchase all required items from the single store. That is the concept in case of bioinformatics pipeline. In the form of a pipeline, you stay in one interface or you work on one website. This is a problem in bioinformatics pipeline. You must have heard of Galaxy, Genome, and that's a stool. But again, depending on your data, depending on your requirement, you still have to use other tools. So, secondly, there are no gold standards for analyzing or interpreting or prioritization of whole exome or whole genome variance in context of clinical interpretation. For example, if you have variants, then there is no set-up XC guidelines for this variant. This is a problem in bioinformatics. There is a lot of scope. The work is going on to develop new tools, algorithms, databases. But again, as I said earlier, the biggest problem is the lack of computing infrastructure. You must have generated your alignment. Usually, mostly those who generate it have data work. They don't feel it. I did a research on alignment generating tools comparison. In that, I take the name of a few tools, such as a clustered W, MAF, muscle, probe, corns. All these tools are used for generating alignments. Usually, whatever I have learned and observed, we use clustered W. Why that person or that person and that person is also using clustered W? I also used it. My study was that which tool is most accurate and most efficient? Before that, I studied probe corns on top. Alignment accuracy-wise. But there is always a trade-off between accuracy and efficiency. If the probe corns were more accurate, it was the same slow. If I talk about it, I took more than 2-3 days on the generation of alignment. Now I had a normal computing machine. If I had a good computing setup, I could have completed all the work in 20 days. But I took only 2-3 months on the alignment generation. After that, as I said, there is a trend. We follow literature less. We talk more about clustered W. I also use clustered W. You can see the literature of clustered W. It is ranked on 6 or 7 positions. Now your work is based on alignment. But the alignment you obtained is less accurate. What about the downstream analysis? After that, what will be their accuracy or validation? There are problems like this. There is a lot of scope. There is an automatic pipeline for analyzing genetic variants. But again, people have published their work according to their lab. It is an open source. You can use it. Your work can be completed or you have to modify it. These are the main steps of the whole-exam data analysis task. When you have a whole-exam and a whole genome, then the major task is to identify the variants and synipses. These are not actually interchangeable terms. There is a lot of difference between these two terms. So you have to identify the variants. The first step is quality control. You have to check the quality of your data. What the issues you may face in the NGS data and the whole-exam data? When you prepare a library, there may be some issues. You may not be able to extract DNA correctly. There may be some contamination. During the preparation of the library, there may be some problems. During the generation of data, NGS machines or platforms itself, if there is a problem, then these kinds of quality issues arise. The first thing I told them is the alignment. This is also a process of alignment. I showed it in the previous lecture. We have a lot of diseases. We have the data of seven, eight camel species. There are hundreds of GBs of data. If you talk about it, on average, there are 150 or 140 GBs of data. You have to work hard with your data and without your quality checking, you can start working on it. The results will not be correct. First of all, you have to check its quality. After that, there will be a sequence alignment. With reference genomic, we check the position of our reeds, where they are aligned. In post-alignment processing, you are checking a kind of quality. After performing post-alignment processing steps, you have actually analysis variant calling data. Then you have the data, where you can identify variants. After that, downstream analysis, you have to prioritize the variants. You have to see the impact. What is the impact of variants on disease? What variants are pathogenic and what variants are non-pathogenic? These are five steps. First one is quality control, then sequence alignment, post-alignment processing, quality control before starting actual work. You check the quality in this, and post-alignment processing. You check the quality again. After that, there is a variant discovery and downstream analysis. This is the pictorial representation of the whole process of genetic variant calling. You are looking at the top left side. There is a fast queue file, which is under quality control on the left side. This is a fast queue. This is a format. Just like the first format, you must have done your work with the DNA protein data. You must have worked with NGS data. The faster format, the gene bank format, and other data. Similarly, when you have NGS data, that data is in the form of a fast queue. Now, you have done quality control. The most famous tool in this context is the fast queue C. Let's look at the fast queue C tool. What is the output? After that, you have the data. The quality is okay. Now, you will go to the alignment. If you don't have it, you can check the quality again. After checking the quality, the data you have, the fast queue C. The fast queue C only reports you what is the quality of your data. This does not correct your data quality. Using the fast queue C, if you see the quality of the data, it is okay. You can move to the alignment process. Otherwise, tools are available. As the list is down here, on the first column, on the last page, using these tools, you can remove adopters, low quality basis. You can trim it. After that, you can see the quality again. What quality is this? In the alignment process, you use tools. These are tools for alignment. Like I just mentioned, cluster W, mass, that those tools are used for aligning normal protein or DNA data. These tools are used for generating alignment of NGS data. You will get the file in the same form. Sequence alignment map, in the same form. This format is a human-readable format. You see the same file. You can read it. You can understand it. But, the data stored in this format is not efficient. After that, you can convert the same file into BAM file. After that, post processing, like you have to identify PC or duplicates, or mark them. After that, you have to improve your quality score. Then, you will have analysis ready reads in BAM form. After that, you have to call VCEF. Like the FASTA format, it is about fast QC. VCEF is a format having variance of your data. In this file, you have variance. After that, you do the further analysis of variance, pathogenic, non-pathogenic, protein, DNA, function, protein structure. This is the form of fast Q format. When you have NGS data, it comes in fast Q format. In this, it comes in the form of data blocks. The first row is one block that you are seeing on the screen. The first row, is read or sequence. What is read? DNA protein sequence. In the context of NGS data, we call sequence as a read. We call a sequence of DNA as a read. It is the identifier of the read. It is the name of the machine. It is the information on the glass in the front lane. There is no need to think too much for the user. After that, in the second line, it is the actual read. You see that this is the data of DNA. This is the actual read. After that, the plus symbol, just alone, or having the same information which is coming after at the rate of a symbol first record a row. After the plus symbol, it can have the same information. After that, it is shown as the characters below. This is the quality of every base. Now, what are the values of these? You will get the literature symbol from the net. The first symbol is 5, 10, 15, 20, 30. After that, there are other symbols. It is a very easy solution for you. You should use that tool. As we are talking about a fast QC, we can use it. This is the actually accuracy by your parameter of NGS data. Fred's score, as we saw on the previous slide, the fourth line after plus symbol, there were some as key characters. There are some values of the farm of numerical values. If the score of a sequence is representing 10, then it is 90% accuracy. If the score is 20, then it is 99% accuracy of your read or sequence. If it is 30, then it is Fred's score. If you go to NGS platforms, on the website of NGS platforms, there is a threshold for data having good quality. If the score is 30, then it is your data. What does it mean by 30? Fred's score is 99.9%. We also talk about NGS platforms. If someone's data quality is 30, then it means the output of that NGS platform, our machine is good. In the data quality, the most famous tool is FastQC. Other than FastQC, there are a number of tools, FastQP, NGS QC, Toolkit and many other tools are available. But the most famous and popular tool is FastQC. It is easy to understand compared to other tools. If you use Galaxy, it is a pipeline. It is an online pipeline. This tool is embedded in FastQC. You can download it. You can install it on your system. It is available as a standalone tool. You can also integrate these FastQC tools in your own application. If you are making an application for your own pipeline, you can also embed these tools. It is written in Java programming language. This is the output of FastQC. You can see that plot boxes that are in yellow colors are falling rapidly when you move from left to right side. This is the 5 prime end to 3 prime end. Look at this figure. On the left side, there is a tick mark and a cross mark. This is for each parameter or according to other sequences or according to other sequences. You can see that there is a mixture of tick mark, cross mark and warnings. This data is medium-sized according to quality. I will go to this website and tell you about the quality of the data. If you have good data, you can see that if there is a bad data, you can see the picture of it. As I told you earlier here, this is a figure rather than to go to various state of this output. You can see that you should move next or not. You can decide. This is one of the good Lumina data and bad data. Now we can see the previous figure and if this is good you can see all the other parameters are tick marks. Very good quality data. In this other figure there are three portions. Upper one is green then yellow then purple. There are three parts. According to these parts, you can see the same output. If your data is graphically represented in green part, then that is good quality and the other parameters are also good. If the data is falling below in yellow part, then the quality is bad. If the data falls below in the purple region, then the data will be bad. You have to repeat a cycle and do sampling again. You have to use the tool to trim the data which can be useful. You can see all the data on the right side is low quality data. Especially that data on the left side is low quality data. The variable quality is 20. As I said, the data should not come in the purple region. If the data quality as we saw in the previous slide how much should be the Fred score 30. What does it mean by 30? 99.9% quality. It will be a very good quality. But if it is up to 20, then again, as I said earlier, if the data is falling above in the purple region, then you have to decide that you have to do sampling on the NGS data generation or you have to trim the data and do your work. These are some steps to be performed in the case of quality control for NGS data. You people know better why adapters are applied. They are not part of the actual sequence. When the data comes to us, it should not be present there. So we have to remove them. In addition to removal trimming can be performed to discard any low quality reeds. As we saw in the figures, the reeds that are falling above are removed. Adopters and low quality reeds. These are the tools. What was the purpose of FastQC? You have to visualize quality. If your data quality is correct, then you do not need to use these tools. For example, we have seen good Illumina data. But if you want to change these parameters, you can manually use these tools. In this tool, we have not listed the tools that we are using after QC. So automatic parameters are also set. When we are using clusters, the parameters are given. The tools you can change manually. After that, Trimomatic tools is using in the domain of biomedicine data analysis. You can use this. There are many other tools. If you go to the website of all these tools, you can obtain the documentation or manual to use these tools or to interpret the results of these tools. In addition to these tools, there are some other packages for QC such as Pica and Shortread. If you are an expert and are working in the army, you can write your own script for removing adopters or unwanted reads or bases. This is our second step as we saw in the previous slides. What was the first one? QC Quality control. We have seen that if the quality of our data is good, then we will come to this step. Otherwise, we will not come to this step. In the future, you will not move further. This is the same concept in form of NGS data quality alignment, as you have aligned the protein and DNA. So the concept is the same that you have aligned your reads with this and actually what are you searching or finding the position of your reads of your data where it is coming from. So let's align that. Again, efficiency and accuracy are crucial step in this step. When we talk about DNA or protein alignment their data is usually small in volume. You can obtain alignment depending on the size of your data. But in the case of NGS data as I told you before usually there are more than 100 GBC. If you are doing a whole exam if you are doing a whole exam if you are doing a whole genome then there will be more. Then there is alignment. As I said before if you have good computing infrastructure then you will get results or alignment quickly. Otherwise you may have to wait for several days. Maybe weeks or two weeks or more depending on your computing machines that is actually doing alignment. At this time human genome is being used or 38 is being used. GRCH genome reference consortium 37 human genome reference genome or NGS data. When we will be performing SNP analysis some of the human genome 19 or 37 are being supported or 38 are being supported. These are the first two. Tools for the alignment of NGS reads boros wheeler aligner VWA Novoline and member These are most popular famous tools for generating alignment of NGS data. When you perform alignment the file you get what is that file? SAM a human readable file or SAM is available but we do not work on SAM after generating alignment like post alignment processing steps or many other steps researchers or bioinformatics who are analysts according to their data or lab are made from pipelines. For example, I took the name of Galaxy Galaxy is a bioinformatics pipeline or genome analysis tool kit there are many other so this is actually a graphical form of a set of commands like I said the pipeline is you give data once on the same website or on the same interface all steps are performed and you get a result you give data and you get data you may have to use a number of commands that is the number of commands or set of commands these commands are this collection of commands called pipeline manually if you are expert in using bioinformatics tools or commands mostly the commands are based on Unix so you individually commands after doing literature you can make your own commands yourself like I said we are using after QC for removing adopters or trimming the data you like to use after QC there is more efficiency there is more accuracy tomorrow we have another tool it is claiming that after QC there are more results and so on so you can make your own set of commands for analyzing whole genome and whole exome data so this set this set as a galaxy interface is given these commands are on the backend we don't have to give those commands or you can do all this by manually giving those commands so SAM file is converted to BAM BAM binary alignment map you can take it from the web you can write it as SAM format there is a header section then alignment section when you look at BAM BAM will not be read it is not readable but it is more efficient it indexes like you have indexed you can go directly to some section in the file or your data after that all your downstream analysis is being used after having alignment file you may perform some post alignment processing steps what are those majorly you do actually two steps in this post alignment processing domain you have to do two steps PCR duplicates you have to mark them after that you have to recalibration of base what is course what are PCR duplicates PCR duplicates when when the amplification is processed then a single read multiple copies are generated which is unwanted what happens to that if you do not mark or remove PCR duplicates when you call variant we have not called variant we have controlled quality after that we have done alignment after that we are doing post alignment processing steps if you do not remove PCR duplicates then you will have many variants which should not have come variants will come which will have reeds so you have to remove them after that the scores I have told you before in that you have to recalibration of those scores okay what does it mean by 30% or 70% of your reads when you get the read back you find that several percent sometimes even 30% or 70% of your reads are identical copies of each other these are actually the results of a PCR duplication so much data you have it is replicated which needs to be removed this tool is mark duplicates mark duplicates mark duplicates mark duplicates mark duplicates constitutes a major bottleneck since it involves making a large number for comparison between all reads this is another computing or bioinformatics bottleneck or problem when you remove PCR duplicates as I told you in alignment it takes a lot of time so this is time consuming work and for this if you have good computing infrastructure this step will be more efficient thus the majority of the effort in optimizing the run time of reads to variance workflow is focused on this step if you do not remove PCR duplicates then your results will not be good in that there will be more variance there will be more variance then the next steps after this there is a kind of repetition for example if you have 1 million variance then if 70% more data there will be more variance this is the step of improving quality scores of the reads which is performed after aligning NGS data this is machine learning approach which based upon empirical data millions of reads millions of variance based on the quality we have seen in previous slides in Fred's score 10% and so on then this quality adjusts the reads and based on that the steps of variant calling becomes more accurate now we have analysis ready BAM file we summarize till now how many steps we have performed after having NGS data in form of reads first we checked the quality to check the quality we used fast QC fast QC only shows you quality does not improve remember this if you give the results of your data you feel that the quality of the data is a little bit low you need to remove adopters and have to trim your data then you have to use after QC tool after that again you should check the quality of your data it is not that you improved the quality you used after QC and you have to use Trimomatic then directly without seeing quality of your data you should go to alignment it is not like that again you have to check the quality after that we have made alignment for alignment there are many tools BWA Baroze, Wheeler, Aniner is the most famous tool in context of NGS data alignment after alignment you have to convert after that you have to do post alignment processing steps there are two major steps marking PCR duplicates and recalibration of a quality score you have to adjust the quality score that NGS machines may have some issues then what do machine learning tools do like you use Feather how do you predict that it will rain or not or how will the weather be based upon historical data of 100 years about machine learning just to tell you that machine learning 20-30 years ago why didn't it become so popular today computer science people are doing machine learning publication and almost everyone will hear that it is working on machine learning 20-30 years ago why didn't it become so popular back then there were algorithms of machine learning but it didn't become so popular because we didn't have data machine learning tools have as much data to learn like we do human learning one observation then we will say based upon 2, 3, 4, 6, 10 observations this work will be like that we also predict that I know it will be like that that's why machine learning tools work with machine learning algorithm their prediction will not be accurate if they are trained with more data then their accuracy will be more then machine learning tools when you give them data they are also learning from it just like human we also learn every time so machine learning algorithms and tools are also learning every time so this calibration now because the data is too much so rather than if we come up with a quality score instead of going there instead of going back do something else then these algorithms adjust our score of machine learning improve quality or you will highlight some rears that this won't be used so after doing these 2 steps we now have a file which we can use for variant calling now next step we will do variant calling variant calling is the process of identifying difference between the sequence series resulting from NGS experiments and a reference genome that means the data you have you have to align with the reference genome human if there is any other animal species it needs a reference genome if there is a plant it needs a reference genome compare with that and then we will get the differences that your data is getting different from here so the difference is that it will be different in the form of a base for example in reference genome G is coming A is coming C is coming there can be some deletions in reference genome there is no base so the difference we call variants this process is called variant calling a reference is a build after struggle of several years after incorporating several information so when you compare and make a difference this is variant calling so these are the tools of variant calling as I said this genome analysis tool is called haplotype callers soap,sneep,sam tools bcf tools this variant calling is not a step if you give a tool it will give a variant calling after processing alignment and pose take a variant or you have to do some other steps so machine learning is also a concept of ensemble learning the recommendation is that it is better to use their variants then use common variants one tool tells you for example 5 million the other tool tells you 50 million the difference is 2nd difference is 2nd difference is 2nd difference is position difference so you combine the results and make a file vcf file so that file will be more robust or accurate as compared to a single tool I was talking about ensemble learning so machine learning is also using a hot approach of ensemble learning so it is the same that you should not take a tool for example if a single tool is recommending 2-3 tools then the level of confidentiality will be high now we will see in the case of synopsis when you do synopsis actually you are performing or you are calculating computing, identifying pathogenicity of synips or variant what is its pathogenicity what is its impact on protein, DNA, protein structure on the function so whole exome analysis if you are using a pipeline if you are using a whole process then the task of the synopsis the 5th task of downstream analysis is the same we do not use a single tool you will have to hear the name of the shift you will have to hear the name of the polyphen you will have to hear the name of the iMutant there are dozens of synopsis and access tools so when you want more accuracy more confidentiality more high level more good results then you use 5, 6, 7, 8, 10 tools if you use for example 10 tools are declaring that this is pathogenic if some of the tools are saying pathogenic and some are saying non pathogenic then you leave it it means that the results are not good there is filtration of variants you do when you have a VCF file then you filter it depending upon your data quality or post process steps there are 2 steps to filter hard filters to the data and variant quality is called recalibration like we did calibration in case of quality in that case also we have recalibration in this case we are calibrating the quality of variants again the second approach is variant quality score recalibration it is actually a machine learning approach hard filtering what is hard filtering is applied by filtering via thresholds for matrix matrix is made for this threshold in this you to filter or to make a final file you define a threshold define yourself tell the tool that this is a threshold you define a filter based on this but in case of a second approach VQSR on the other hand relies on machine learning to identify annotation profiles of variants that are likely to be real it requires a large training data like I have told you the history of machine learning algorithms that these machine learning approaches were also available several years ago but at that time it was not useful because we had less data so minimum 30 whole exam data that is to apply VQSR variant that you have to calibrate and filter using machine learning tool in that that tool and algorithm that has 30 whole exam data that is to train from this data train machine learning tool that if this thing comes then you have to take the variant keep it if this type of data comes then you have to discard it so this 30 whole exam data as I have told you the whole exam data usually is in more than 100 GB so this is a lot of data and well curated sets of non variants manually experts have finalized variants like you do BLAST that your query sequence matches with the database okay all this information is in the database similarly this curated sets of non variants so the database of non variants is available their annotation, their information their quality and so on then you filter your variants using VQSR the accuracy of variant calling is affected by coverage tools for assessing coverage information include genomes as a tool bad tools and so on coverage is defined in two context coverage you define the coverage when you are taking the NGS data you have to take it I need 70x coverage I need 70x coverage the coverage is used when you have the data the coverage affects the accuracy of variant calling I have coverage definition in both context coverage is defined as the number of sample nucleotide basis sequence aligned to a specific locus in a reference genome that is you have a reference genome from that one position the term is called in form of alignment what is the position column that is if you have this the number before what is the position of T the first T for example 1 is H position 2 is E position 3 and so on on one position the basis of your alignment is the coverage this coverage is based on the coverage when you obtain the NGS data the number before the X is the coverage the average number of times your genome will be sequence when you give coverage time for generating NGS data you tell me that I need this much coverage means every read I need 30 copies I need 40 copies how much I need that is the coverage variant annotation what is annotation you have heard the word what does it mean by you have I will tell you annotate the data you have for example I have seen many pictures if there is a gene there is a mark on the start the second mark is open reading frame the third mark is stop the next mark is gene if these marks are not labelling if they are not labelling then we do not know what is in the data we have the data it is in the form of a string by seeing a string what can you tell we can label it we annotate every part of the sequence we tell which part of the sequence what is the name what is the benefit so that variant annotation means which gene which gene which gene is found what is the impact which disease can cause what will be the impact on the protein structure and there may be several useful information about a single variant so we call this variant annotation position position can you come to the position can you come to the position characterization you can say meta data a sequence a variant about your information you can read you can understand what is this like the name characterization or in term of if I talk about db in computer science field it is called meta data about the data this is the concept of annotation without annotation you can predict the impact you can't predict you can't understand you have no benefit correlation of the variant with non genomic annotations with database like I gave the last example with the database this is the information in NCBI this is the database this is the information the severity and impact of these consequences are often indicated using qualifiers low, moderate, high this is all about the impact of a variant today we will do a little hand zone in that you will see a heat map or someone else usually when you tell the impact of a variant you will tell if it is high or low for that all the tools prediction of single nucleotide variants to name a few polyphen 2, LRT mutation taster as I told you these are all tools the impact of a SNP these tools in my second and third slide I wrote a research area comparison of pathogenicity tools those tools that predict the pathogenicity of a variant you can compare these tools I will tell you how to compare these tools ANOVAR SNP variant effect predictor as I told you all the tools that we are looking at exam data analysis or whole genome data analysis all these tools you have to use to get the final results the somatic genomic variations now I was talking about germline mutations there is a little bit difference between analysis of somatic genomic variations and germline variations approximately 70% to 80% is the same same workflow what is the difference sequencing both tumor tissue and a matched normal sample both of you will sequence in that case you take one sample in case of somatic genomic variations you will take two samples one corresponding normal tissue sample and one effective tissue after that the rest of the steps are the same now you are doing two things in addition to reference genome alignment you have to do both but in case of germline mutations we do work only on a single sample but in case of somatic mutations we work on two samples one affected and the other normal variant column what is the difference where both the tumor and normal process read data are utilized to identify both of you will call the variants that are present in the tumor not in the normal then the variance call you have to compare with reference genome then the variant column you have to see which variations are coming in the normal there are variations you have seen one workflow one pictorial representation of somatic data analysis and you have seen the difference can you tell what is the difference only the difference is that both are going together normal and tumor are the same steps are the same you will do the same steps the same these are the tools for that number of tools for cancer specific annotation for cancer there is a lot of work on cancer cancer in the name of genomics there will be a domain like bioinformatics when there is a lot of work this domain is emerging in the name of cancer there are machine learning tools cancer specific they are made from pipelines websites consortium due to importance of this disease structural variations germline somatic structural variations size compared to germline or somatic mutations most important are copy number variations copy number variation is a frequent form of a critical genetic variation that results in an abnormal number of copies of large genomic regions you all know that chromosome rearrangements or copy number variations a significant part of your genome delete insert copy clinical interpretation of genomic variations one of the most challenging process in analyzing whole genome data is the clinical interpretation of the genomic variations that is important in form of monogenic or complex disorders and personalized treatment of such disorders it is still a challenging task clinical interpretation is actually driving us towards the personalized medicine in Pakistan sequence based reports are given now we take clinical reports like CBC, LFT, RFT or other reports now some labs have started working on commercial diagnostic laboratories now maybe they are not bringing it to the public they are making their own infrastructure as I said it is very important to have a computing infrastructure that high performance computing machines for example if you have experts they are working on it now we give the public sequence based reports that as we have done all the work here we will take your blood sample we will do NGS and we will tell you the differences in your genome what is your current predictions in the future what kind of diseases you can face there are a lot of machine learning tools that predict your future diseases and health so in this when you will do its significance or interpretation of variants then the personalized medicine will be very very useful and easy to do clinical interpretation these are three guidelines American College of Medical Genetics and Genomics has given a document you can read it search it on google you will get it so all the variants will be like this so how to interpret it you can read it and your opinion society for human genetic guidelines there are three kinds of consortia and laboratories or institutions that guide you how to do clinical interpretation these provide the standards and guidelines for the interpretation of genomic variations and include evidence based recommendations on aspects including the use of literature and database and the use of in silico tools criteria for variant interpretation and reporting these are the guidelines based on literature based on database as we have seen of variant annotation so in this way all the information is given by using tools how to interpret it following are required for the interpretation of genomic variants variant dependent annotations such as allele frequency 1000 genomes exact genomes databases and tools used here to calculate the frequency of alleles the predictive effect on protein and evolutionary information in conserved regions if there is a mutation or what is the impact of a variant after that disease dependent enquiries such as mode of inheritance what is the impact from the perspective of disease course aggregation of variant with disease within families if there is a disease generation after generation that you have to interpret prior association of the variant gene with disease then pathway analysis pathway analysis has a significant or important role in interpreting variants the pathway analysis is sometimes it happens that the gene in which you have a variant is not directly involved now we want to see how many genes which are working in a complex combination and how they are impacting the disease pathway analysis for that the databases are human genomic variant cosmic or excellent resources all these interpretations or variant annotation or your impact to find out tools in interpretation of these variants all these tools are given for personalized oncology purpose numerous cancer specific tools exist we have only two or three slides then after that my theory lecture will be finished and we will have tea break after that we will have pathway analysis is another powerful component for interpreting genomic variations it is a group of methods in incorporating biological information from public databases by grouping long list of genes number of techniques and number of genes you analyze the complex how those genes affect the disease these are tools for pathway analysis thank you this slide this slide is relevant to analysis of SNIP we will do a hands on after-tree I have taken SNIP's data and used SNIP tool and used cleanvar to do pathogenicity quality after-tree thank you very much excuse me let me start during tea I have a couple of colleagues saying that your lecture is very interesting but we haven't moved the genomics yet so I said let me tell you I have a take home message you will work on it at home just one or two days after that and it will be very very useful for you people my own experience I am actually a computer scientist not a biological scientist but I took a sample of sequencing I passed it through for example yesterday there was something about Moringa Olifera we made a whole genome by sequencing and made a genome and thank God we have submitted it in NCBI from Pakistan thank you very much so there was so much difficulty that the project was only a year but it took 2-3 years there was a corona there was also a reason for sequencing the data was sequenced which were our vendors they were asking for money money was transferred to the dollar and our new Pakistan dollar it took a long time and after that when we got the data I have called two major challenges one is computing infrastructure lack of computing infrastructure second is capability so we learned from the lumps we helped maybe from the nests we took a tourist help we were successful but it took so much time and I am telling you about the battle lab but in the case of biometrics I will show you maximum 2 months 2 months and your 3 impact factory publication is ready but if you involve the other battle lab then the samples were sequenced there were errors there was contamination they went in the cycle and then it takes money and then you are able to publish it so this is a tool that you will learn today you can do it your students we will be always available for collaboration and helping your students so for that we have computing infrastructure and Alhamdulillah capability is good for us so pathway analysis then molecular simulation and many others so today the slide that you are showing is a paper published in PLOS 1 you know it I have 4 impact factories so all this work I took this image and it will take around 1 month or 45-60 days this work is more than 60 days and you will not have to move any other place sitting in a seat sitting in a good mood the data is available the guidance will be available there is no problem so the first step is SNP data from dbSNP and protein structure from PDB you have to select a gene the work that comes up you have to select which gene you have to analyze okay the gene is final any gene is final after that you have to go to the website select dbSNP and the name of the gene will show you all the SNPs after that the major work like in this figure you are seeing that there are two parts of this research work one is on the left side and the other is on the right side the work on the left side is more a number of articles dozens of articles are published on this research work genes are different work or workflow or steps are the same for example I have worked on gene A you do the same work on gene B the third person has the same steps the same workflow take the third gene so the right side is the untranslated regions variance some people include it maybe this is less important we have more important variance coding missense variance their missense variance or non synonymous variance nSSNPs on this figure in silico analysis of SNPs associated with the name of the gene they usually analyze missense SNPs or non synonymous SNPs there are two things one is sequence homology and the other is structural based tools in this study three tools have been used for analyzing SNPs when I will be talking about the analysis of SNPs it means that we are identifying our highlighting impact of SNPs on protein structure or function so shift have polyphen two are IA mutant sweet these three tools are used in this study some studies have used 5-6 tools some have used more tools I had seen work on this study it was the nature it had 5-6 factor it had more than 2-3 scientific reports in that there were 20 tools on this work these three tools look there is no one tool of sequence homology there are more tools there are only two tools it has machine learning base it has made a set of tools of sequence homology it has used three tools structure homology it has used these three tools machine learning deep learning it has made a set of tools it has taken 3-4 tools so it has made 15-20 tools it has desys it has data more volume then it publishes these three tools these tools will tell the pathogenicity of the variants after having the impact of variants now you have to see those variants whether they are in conserved position you should have better knowledge that if there is any in conserved region it will have more impact let's move forward that is the third filter it has used three tools it has used a snis it has used fift polyphen for pathogenicity after taking it it has derived a common variant which means the variants three twos. If you have, for example, the 500 snips, so after these steps, you will have only five, six, seven snips. After that, she used a concept tool. This is a conserved region. It tells about snips that you have identified snips in the conserved region or not. If there are, then they become a little more filtered. After that, the molecular modeling. The steps above are acquisition of dbSNP data from dbSNP and protein structure from PDB. What is the protein structure of that gene? The protein of that gene that you are studying. Now, when you do molecular modeling, what does it mean by molecular modeling? Computational modeling. Homology modeling. This is a sequence whose model or protein 3D structure is not available. Then you choose molecular modeling technique. PDB is a protein data bank in which the structure of the protein is available. Identified through experiments like NMR, crystallography. The protein structure identified based on experiments is the protein data bank. This is the molecular modeling. You see, you have a protein sequence. There is a variation in one place. Now, the structure will be different as compared to the wild type allele or protein sequence or regional sequence. Now, after applying the concept of molecular modeling, you are doing the sequence in which there is a mutation or mutant sequence. You are actually doing molecular modeling of mutant sequence. Now, you will compare. There are a number of tools which provide you a facility of visualization by rotating protein structure. For example, if there is a mutation on position phagism 206 or its structure or how it feels. And the regional sequence, its structure, if you get it from PDB, you will compare its structure. After that, after using molecular dynamic simulation, you do the variation or mutation. You do the through simulation impact study. Similarly, if there is a variation in our body, we get a disease. Now, you have to simulate it. If there is some mutation or variation on the gene, what will be the impact? Then the simulation will tell you. So, these are the common steps which we use in all studies. In today's talk, I will tell you the methodology to collect data about SNPs and usage of shift or polyphen. And then I will show you the clean war database that have reference SNPs or validated SNPs for analyzing pathogenicity tools and CBI. First, let me show the shift tool, SIFT, Shift Predict Effects of Non-Synonymous Emissions Variants. Here, Shift Non-Synonymous Single Necrotide Variants. This is the interface where you will actually give your SNP data. Now, where you have to give your SNP data, which you are going to analyze, which you are going to highlight is its impact on protein structure or function. What format do you want to give? This is the sample format given in this. One, the first digit is showing the chromosome number. These are comma separated values. First value, first digit, our numerical value is showing chromosome number. Second position, chromosome number 2, 3, 4, etc. What position has changed? Third, the numerical value has that shows forward orientation or reverse orientation. Fourth and fifth, this is for the wild type allele and mutant allele. Before C, now G has come there. If we talk about first record. Second, chromosome number 1, then position, then forward orientation. Then mutation has come there, variation has come there. Before A, now G has come. Third, before A, now C has come. Now we have to collect these values to run the shift. For this, you go to NCBI. From here, you have to select DB SNP database. SNP database has come. Here, any gene name is given. For example, I will give CYP11B2. Tell me, what is the name of it? BI3. BNIP3. See what are the total number of SNPs reported till now in this gene. 6,616. We have to collect only miss sense SNPs or variants. On the left side, there are filters that you can apply. I select miss sense here. Let me show you the miss sense variation in this gene. Now there are only 159 genes. Approximately 7,000 SNPs have decreased. Miss sense variants have 159. If there are other genes, miss sense variants will be more reported. This page is showing you the miss sense variation. Next, these are their fields. This is the first one. RS1050740. It is the ID of this variant. Reference SNP RS stands for reference SNPs. It has some numerical values. It has an ID. The way you know the accession ID in the case of DN, that uniquely identifies a protein or DN sequence accession ID. In the case of a DB SNP, you will get RSID in the SNP database. After that, there is a variant type. I have told you that TE and C have been reported. In one study, A has been reported. In another study, C has been reported. Chromosome is the number. In the case of a 38-reference genome, 10 chromosomes have been given. The same chromosome or position in the case of a 37-reference genome has been given and so on. If you click on this RSID, you will go to the next page having a detailed description of this variant. You have entered in the database of a DB SNP. There is all the information about it. All alleles are reported in the forward orientation. This parameter has been given to you in today's lecture. It is said that it has been given for 15-20 minutes. After a lot of struggle, we have found out something. Forward orientation. In the case of a shift, I have shown you the third parameter. This is the one I have selected. One will be in the case of a forward orientation and zero will be in the case of a reverse orientation. If we see the forward orientation on this page, if it is written here that there are synapses in reverse orientation, then we have to write zero there. Now I am going to make a list for the shift parameter and how you have to collect the data. If I open the notepad file, I am going to write it together. Look at one more. If I go back to this, what I told you earlier, shift is supporting only 37, reference genome, not 38. Now we have to collect relevant data of 37 genomes from the website. This is the date of 38. If I go to its classic site, you will find some data from there. You have also found 37. The integrated maps, the column you are seeing, the table below this, that is showing data of 37, reference genome as well. What is chromosome number? 10. Position is this. I will copy the position from here. I will do it once again. Then I will show you again. Chromosome number 10, I took the position from there. What was its orientation? Forward. What was its allele? I will go back to the topic. T and A. I came from here. I copied the switch to classic site. We came to this page. This is also written. Riff, ref, Sniperlears, A, G, T. After that, Ancestral, A is written. You can write T to A. T, comma A. This is the format of shift. Now, I have selected one parameter of SNP. Now, you can give it a shift and run the shift. I will copy it here. And upload file containing chromosome coordinates and nucleotide substitutions. You can make a file here. For example, I am making this file. I am making this file. If we want to make a順 one, we must write another in a slide, as it is called, we will use the relevant you get the results. Luckily, the shift has given the results early. But sometimes this is also a setup. We have queued, the people around the world are queuing, then they get the queue in line. You might get the Gwantepad results or you get a little more than that. Now, here the results have come. For us, this is more. Tolerated 100%. Damaging 0. What does it mean by that? This variant is benign. There is no harm to it. It is non-damaging, tolerated. Now you have made an Excel file, made a table in Word, adding the shift results, writing the RSI, writing the results with it, so that other parameters can come in your mind which will help you later in analyzing the results. So, in this way, you will get a file. Now, we are taking the results of one tool. I told you at that time that there is a wild type of LTE, A has been reported, C has been reported. No, no, no, then you will have to make another one. Then you will have to make it with C. Yes, you will have to make it with C. Then you will have to tell in your article or thesis that this is one, there are two reports of Aleel. You will tell them separately. This one, this one. This is for forward or reverse orientation. I have shown you here that when you are on this page, it is written here that all Aleels are reported in the forward orientation. Instead of forward orientation, you have to write one there. If there was zero orientation here, then you would have written zero there, sorry, reverse orientation, then you had written zero there. One, zero. Yes. When you are actually collecting parameters for sifter, then first you will come to Coromossum number, Coromossum position, then for forward or reverse orientation, one or zero, then after that Aleels, that is, by putting slash, wire type slash mutant Aleel. So this was your question, that you will do all this work for 159 sifts. Yes, you can paste it in that box. You can make it once. No, this sifter, it tells that Yes, it will give it all separately. It will give it separately. Yes, it will give you such a table, give you some space or line, it will give all the variance results. It will give such a box. I will repeat it once again. I copied the gene's name. I am closing all the windows. You have to go to NCBI. From here you have to select SNIP on the database. Here you will write the name of gene. It has been selected before MissSense. That is why it is showing 59. If I unselect MissSense, it will show the total variance which we saw before. I copied MissSense again. Now here you have to write the name of the gene in the file. Rather than to remain on this page, or you have to work later, or you need a file, send to, click this. It will copy all of these, or make a file. Download 159 items. Format. Summary, XML, tab. Let's take the summary and see. I just mentioned RSID. Create file. It has given all of these. You have a file there. You don't have to go to that page again. You can take the Notepad file and do some work. After that we clicked RSID. RSID. This is the RSID of all SNPs. Reference SNPID. RS stands for reference SNPID. You are seeing this. This is the second SNPID. This is the ID of the use. This is the ID of the use. You have to click this. You will get the orientation parameter here. You have to put 1 or 0. You have got this. 37. Because Shift sports 37, reference genome, you will get the data from here. This is the Muslim number. This is its position. And we also got Alice. We also got its orientation. These are 4 or 5 parameters. You can make a file and give Shift. After that you can order the results. There is another view here. GeneView. This is a classic website. From here. If we click GeneView, this is an older website. It was from NCBI for many years. We will delete it. But it is still showing. If we click GeneView, it will take the clinical source of SNPID. It will take the gene region. You have to take CSNPID. It has frequency. You have to take something double hit zone. You have to do coding. C for coding SNPID. You go. Now you will get this on a new page. In which all SNPs are in a tabular format. That is more readable as compared to the home page of NCBI. You can see up here. You get a lot of information here. There is chromosome position. MRNA position. This is RSID. After that its function. What is SNP? SNPID. Variant. All this is showing you. Amineser position. You will get a lot of help from here. Now I will show you the polyphen. Polyphen 2. This is its interface. You will have to take the data for each SNPID. We need protein and SNPID identifier. You will give protein sequence in FASTA format. After that you have to give position. It is a wire type allele. It is a mutant allele. You can write some comments here. If you want to write in the description. Otherwise, this field, that is the last field, query description is optional. How to take these parameters? We took chromosome coordinates. In case of polyphen, we took protein data. We were here. I came back to that page again. So that you can revisit it. You have written it. Now you are seeing polyphen. We need protein sequence. We need a position. We need a allele. For that, we have T and A, T and C. Position. Let's go to the classic page. Classic switch to classic side. This is a part that is important for our polyphen. We need protein data here. In case of polyphen. It is a section ID of the protein. I open it in another window. Position is 143. Let me give it here. What are the alleles? Protein. RR. Both are the same. If I select another one, I am going to the other side. Just to show that it is the same. Someone else can come to the other side. The difference is L and Q. Position is 113. Select L here. Select Q here. Let's see. A, A1, A1, A2, A1, A2, A2. The first one is the wild type. The second is the mutant. Select the position. Let's give the sequence here. I am giving a new window. faster format, you have to copy it, this one, you have to copy it from here. Faster format means, what is polyphen, you want faster format, so how polyphen will recognize that the given sequence is in faster format with this greater than symbol, we have to take it from here. Now our parameters have been completed, let me submit it, click on this button, it is your choice, it is optional. Let's see the results a little later. This is an iMutant, I have shown you a tool, in which you have given your parameters based on the given sequence, I have shown you a polyphen, in which you have given your data based on the protein sequence. Similarly, when you use 5, 6, 7, then more and less, with a little difference, the parameters are the same. So you can do the rest yourself, you will search on Google, you will get a lot of articles about the analysis of NSSNAPs associated with the gene. Like I have shown you all the pedagogy and protocol, what are the steps for analyzing SNAPs, you can do any of them. These are the results, completed. View, this mutation is predicted to be probably damaging. Now the heat map you are seeing, this is showing the severity level, the heat map. If you go to the left side, it is green, then it gets red. At the end, its 0.99, then it shows the specificity, sensitivity. So this is damaging. You take the same data, give the shift, see what it says. For example, if it says pathogenic, then you will go ahead. If it says non-pathogenic, then you will leave it. As I said earlier, usually you analyze SNAPs using 5, 6 tools. And those SNAPs that are called pathogenic or maximum non-pathogenic, then you assess the difference. Like I told you earlier, use the concept, do modeling, then do molecular dynamic simulation. Damaging. There is no need to go into that. Look at a heat map, if this black bar is coming on the map, it is just a little ahead. It could have been a little ahead, the severity level is higher, but you can write damage in your studying. It doesn't have to say that it is damaging. It doesn't have to say that it has crossed the green bar, then it has started moving towards the damaging. Now this shift, polyphen to iMutant, as I told you earlier, I saw that you have made a sequencing, after sequencing, you have identified the variants. Now after identifying the variant call, you do this step, what we are doing. The pipelines that are there, they do it for you. You will see that there are shift results, iMutant or polyphen results. There was one area, research area, which I showed you in the first or second slide, that today we will work on three research areas. You have raw data, you have a variant call, and in that you have two opportunities, that you get unique SNP, you get SSNP, which was not reported as damaging. There can be a publication on that, or you can identify a gene, after following the whole process. And secondly, this is a standalone, in case of this research work, you don't have to go to wet lab. In that case, you have to go to wet lab, or you have to do a whole-examination, or a whole genome sample, or you have to get an ingest, then all the work is done. In this case, you have available data, tools available, you can do it. Third thing is, now you have to see, there is shift, iMutant, polyphen, there are many tools, which of them is more accurate? The comparison of these tools, is one of the good study. In this, the good study, you have to compare them with three perspectives. One comparison of memory used by the tools, for example, shift, 7 GB memory used, polyphen 5 GB used, iMutant 3 GB used, so you give a comparison like this, which tool is more efficient according to memory? After that, efficiency, as you saw, shift gave 4 resort, polyphen also gave, but there was a difference, so that is your efficiency. Third accuracy, which tool is more accurate? Now, when we talk about which tool is more accurate, it means, we should have some reference data. Reference data means, we should have such SNPs, which are either declared that these SNPs are pathogenic, proven. Then we will give the proven SNPs to these tools. For example, we have 100 pathogenic SNPs. Now, we gave 100, the shift said that there are 90 pathogenic, 10 was tolerated. So, the polyphen gave, 95 was called pathogenic, iMutant gave, 85 was called pathogenic. I am quoting just examples. Now, based on this, you will tell their accuracy, which tool gave 100 proven pathogenic declared SNPs, which tool gave more SNPs than that data, it means that it is more accurate. Now, where should we take this reference data? So, this was my third day in today's lecture. You will write here, right? This is a database, it is a web portal, where they have these SNPs. So, you can make a quvery. You can use it to help them. They have taught me to make a quvery. Today, I have brought this thing with me. I have copied this. In search board, you will see this quvery. Here it is written pathogenic. So, here it has shown the result of pathogenic. 13,364. This one. Now, below, you can use all these filters. To narrow down, this is a lot of data. We need a good type of data. Molecular consequence, miscellaneous, take it from the instance. Select it. In variation type, you take a single. We do not need deletion, duplication, insertion. We focus on a single SNP. Select this. After that, variant length, less than 51. Select less than 51. It will make a difference here. In review status. In review status, what you have done in bioinformatics, a term is called manually curated databases. Or manually curated alignment. What does it mean by when we do alignment using cluster W or some other tool, that alignment is not accurate. It is not accurate. Our work is easy. After that, experts do the alignment themselves. There is a lot of time left. In terms of efforts, time and money. When experts do the alignment, that is called manually curated alignment. Or some other data. When we go to review status, in review status, there is an expert panel here. That is, the database that they have made, NCBI's one database. And the experts have validated these SNPs that these are the results. They are the pathogenics. Now click on this. Now you have the 13,000 that was coming. You have 522. You can narrow down the filter by using for example, if you select it from here, it will be 56. After that, if you do it in method time, this is the table you are showing. These are the SNPs that are validated by expert panel of NCBI. NCBI. Now again, from here, see the chromosome position is given. This is the chromosome number. This is the position. This number was based on the 37. This is on the 38. After that, this is the gene given. After that, you click on this. You will have some more information on the SNP. This is the ID of the gene. Then the chromosome is with Ali. With the position. This is the ID of the T. This is the ID of the SNP. This is the ID of the DB SNP. Where we were before. You will click here. You will go to the DB SNP. Where you will get the protein sequence. We also took the position. We also made all the coordinates. In this way, you will collect data of these 1200 and sorry, 512 SNPs. This is a reference dataset of SNPs or proven SNPs. Now, you will give all these SNPs to the shift, polyfan or eye mutant. From there, you will get accuracy. Some articles are published on this. Again, there is a scope. The developers appreciate this. They are saying something about our tool. We are guiding how much accuracy of our tool is. How much efficiency is. According to memory and time. Yes, someone has someone else's answer to this question. I did not know. I told you earlier that these tools are shift eye mutant or polyfan. Even alignment generating tools cluster W, mass after muscle. Tools do not give 100% accurate result. This is one thing. They help us. They expedite our work. For that, I said, this shift is not 100% correct. This is what we have given to SNPs. Now, we believe in the shift. Polyfan has told someone that non pathogenic we believe in it. Polyfan is right. What is the accuracy level of these tools? I said, this is a study that you should check the accuracy. How can we check when we have reference data. That data is either pathogenic or non pathogenic. Now, we took pathogenic data and we know that all SNPs are pathogenic. Now, if the shift is 100% correct, then shift should declare all these SNPs as pathogenic. Then someone should not declare non pathogenic. But the shift will be pathogenic. From 512 SNPs it is possible that the shift is called non pathogenic. Same case is with other tools polyfan or imutant. They will not say all of them. There will be a difference. Now, your false, positive, false, negative, true, positive, true, negative, precision, sensitivity, the statistical parameters are there. Based on this you will tell their accuracy. As I said in case of a cluster W that we from our teacher or from our colleagues or from our class fellow we are also using cluster W but cluster W's accuracy is ranked on the 8th number. So now you have made two trees, one of you made cluster W after taking alignment one of you made tree after generating alignment from probe count. Which tree will be most accurate from probe count? Similarly, when you do homology modeling from the probe count and cluster W's which model will be more accurate from probe count? There are many other things which are based on alignment. So the same thing is that I am using shift I say on the basis of shift that this allele is variant, it is pathogenic or I tell it that it is non-pathogenic I should have knowledge that how accurate is the shift or how accurate is the polyphen. This was a third study. I also have a problem. So I said in case of selector gene we got 159 snips if you put 4-5 tours on it you will have 3-4 snips for further analysis. In the first step you will get more than 150 snips. I said that the snip you got after doing complete analysis after annotation you will know whether it is novel or not. If it is not then it is your contribution. Yes Yes It is your contribution. Yes This work that we have done with the whole exam data analysis you will get 9 snips. Yes It means that non-pathogenic snips should be called non-pathogenic. You are talking about accuracy then they should say non-pathogenic. Then you will study from that perspective. Yes Thank you Thank you so much sir for a very informative session. Ladies and gentlemen this brings us to end of the first session of the day. Now we will be taking the one hour lunch break and prayer break and we will resume the session at 2 p.m. sharp. Thank you Thank you Hello Good afternoon Is anyone on the other side? Are you there? You are the only person whose voice I can hear. How are you? I am fine I think the lunch break is going on so that is why I am here. No problem Thank you Thank you for telling me. Thank you Hello Hello Yes, very much so. I am here. This is Samarumta from Aarik. How are you? I am good. Very nice to meet you. Same here. Let's start our second session of the day. Are we 5 minutes early? Let's wait for 5 minutes. Let's wait for 5 minutes. Let's wait for 5 minutes. How was the morning session? How was the morning session? This is day 2, right? Yes, it was day 2 and it was very informative. Participants learned a lot. It was also an activity based. Excellent Very nice Very nice So basically, for my understanding the colleagues who are listening to this I can see they are all sitting in an auditorium very nicely comfortably after lunch break they are all sitting comfortably It's very nice to see you all So for my understanding some of the colleagues are sitting in the auditorium some of the colleagues are listening online How is it working? Madiha We have physical participants at auditorium here in Virgil University and our other participants from other stations are on Zoom They are on Zoom So if I want to ask a question or if I want to interact with colleagues what is the best way Can I You can ask a question and we have a mic so you can talk anyone Perfect So the colleagues sitting in the auditorium are all listening to me? Give me a wave everyone Okay Fantastic If I ask you a question can you give me a shout out for example if I ask you what did you eat during lunch Can you tell me You have to go to the mic Who will be brave to tell me what did you eat during lunch We had biryani Very nice Amazing And kebab Excellent That means a good start to the workshop already I think we had sweet rice too Was it halwa? Halwa Amazing That means Virgil University is looking after you very nicely Biryani and kebab and what not Zabadas Summer can I quickly share my screen just to make sure that everything is working well and then we can start in about 2 minutes Sure Maria Please let me know when you can see this Okay Yes we are viewing it Okay fantastic So we will give it maybe another minute and then we can start Let me know when you are ready to start and then we will just make a start I will introduce you then you will continue Perfect thank you Whoops I think I did something Which screen you can see Academic writing skills Yes Yes Maria we can see And can you see this slide 1 of 55 or no There is no number on slide So only thing you can see is this big slide right Yes Academic writing skills Okay ladies and gentlemen welcome back We will now resume our second session of the day Our speaker of this session is Miss Madiha She is a fellow of the Higher Education Academy UK and works at Imperial College London in the capacity of undergraduate education manager Her profile includes working on regional, national and international projects on education career development, women in leadership and support for families Miss Madiha and she has previously worked in a varied roles at UCL on several working groups including the Gender Equality Committee Springboard for Women Committee and UCL Aetna Forum She also co-leads the University wide initiative of Aetna Swan which is an award in recognition of the university's commitment to advancing women's career in science, technology, engineering maths and medicine, let it stand Madiha is also the founder and chair of UCL parents and careers together Network for which she has won the prestigious UCL Excellence Award for showing exceptional leadership skills in supporting parents at UCL Today she will deliver her talk on teaching academic writing and critical appraisal to undergraduate students I welcome you Madiha on behalf of Virtua University of Pakistan Please proceed for your presentation Thank you very much Thank you very much I welcome and my salams to everyone who is listening All the colleagues who are sitting in the auditorium all the colleagues who have virtually joined Thank you for coming to this session after your lunch break because I know that after a meal sitting in a session is a heavy job Thank you very much for being here today In around an hour or 45 minutes we will see how it goes I will be talking to you about academic writing skills and critical appraisal skills for undergraduate students Because of the layout of today I think some of you are in the auditorium some of you are online I will try to ask you as many questions as possible and if possible talk to yourself who are online and who are sitting in the auditorium please take the mic and do speak with me because this is going to be a two-way conversation Madiha is online they cannot unmute themselves they can put questions in the US section no problem at all so basically you will see on this slide it says Imperial College London at the top but you will also see my twitter my name is Madiha this is because I was not getting a name that was available on twitter so I just stayed with what it is so my name is Madiha I am the education lead for Upsign I will talk to you about Upsign in a minute I am also the gender equality lead for my institution academically my background in international development professionally my expertise is in educational leadership in equality, diversity and inclusion and in supporting students and I am also professionally very very interested in gender equality improving the career progression for men and women outside of my professional sort of a zone I am also a mother Madiha she is 17 years old she has gone to school I have been born and bred in Pakistan I moved to England about 16 years ago media education Allah has been kind to me I am so pleased that I bear the Pakistan flag when I work at Imperial College London which is actually one of the best universities in the world so our conversation here today I am also wearing another hat of Upsign I will tell you about Upsign in a minute today's conversation is roughly going to be in three parts the first part is going to be a brief introduction to Upsign because I am also wearing the hat of Upsign today we will then move on to critical appraisal skills and then we will move on to academic writing skills we will stop halfway through we will take a five minute break and we will just see how it goes in the UK Imperial College London the position here is it is about supporting undergraduate students and their education and that includes everything right from day one when they send their first question about how we will get admission and talking to them helping them choose the right degree when they start to apply for the place then supporting them with their application when they arrive into the UK helping them settle into university life and after that with international research with their assessments their lectures everything in between after that when they graduate then they become part of the alumni network so my job is to look after their student journey right from day one all the way up to graduation and it is a very interesting position because every day I get to meet different kinds of students from all parts of the world from all over the world from Malaysia, China, Pakistan from India, Sri Lanka from between the UK so every day is a different day every day I learn something from them because it is a very international world we all live in and one thing I have always seen is that when our children who come from Pakistan particularly undergraduate they have to work harder to get up to the mark about their research skills because in Pakistan the research skills are a different way of teaching them the framework of teaching them the research skills in the UK are a different way of teaching them why we based learning is completely different so today's conversation is going to be a bit about the core skills you can teach your undergraduate students how to do critical appraisals and how to do academic writing is everyone with me? if you are with me just give me a thumbs up so I know everyone is listening to me I can see people I hope who are listening online will be thumbs up okay so moving on the first part which I want to quickly talk about is UpSign Network UpSign stands for UK Pakistan science and innovation global network today I am here representing the UpSign Network and Imperial College London so UpSign Network I just told you in the beginning I am the education lead for UpSign UpSign is a network of researchers academics, professional policy makers, practitioners thinkers, solution makers we are basically a network based in the UK and our job is to connect UK and Pakistan academics we work to address the social and economic challenges of Pakistan and Pakistani diaspora here in the UK and our job most of our objectives they are framed around the United Nations Sustainable Development Goals the UN SDGs I am sure you are familiar with these it is based on these 17 goals particularly I am the lead for goal number 4 and 5 number 4 is quality education and number 5 is gender equality I am an educationist by profession I have a vested interest in sharing links between Pakistan and UK so that the best practice in Pakistan that we bring it here and the best practice in the UK we bring it to Pakistan hence this workshop today number 5 gender equality my personal interest like I told you I am a woman I am born and bred in Pakistan I have a daughter after 10 years when my daughter came to the world the world is a slightly better place for her in terms of gender equality and that she also gets paid the same money that men get paid so no gender pay gap how does up sign work overseas we are addressing Pakistan's global challenges we work with Pakistani stakeholders government, universities public private organizations NGOs for example today's conversation today's session is also part of how we work with Pakistani universities and we want to facilitate knowledge transfer and we want to do capacity building of professionals and academics in Pakistan in the UK we do a lot of mentoring and supporting UK based British Pakistanis because the Pakistani population here they need a lot of mentoring particularly our children I think this is our responsibility to give them the roots and the recognition that their homeland is Pakistan and they have strong links with Pakistan we have a team I think this is a slide there are 8 core people who are part of the core team the female professor Parveen Ali she is the chair of up sign she is an amazing woman she is the first female professor in the UK for nursing I think it's a big honour for Pakistan the academic she is now a professor here already there are very few female professors so quickly giving you some examples maybe you came across this last year we launched a training program Pakistan's global graduates the idea was that to give them the skills to come up to the same standard as on an international platform to make them ready for global research or six sessions critical thinking, academic writing intercultural competence networking skills, presentation skills CV writing etc we are also doing something about PhD doctoral supervision there are four segments to it industry partnership, governance interpersonal skills etc in the process of planning this few other things that we have done effective personal tutoring plans or ideas developed we are working on giving excellent feedback to students how does formative and summative assessments work what is the feedback loop etc and then my personal favourite is we are also planning programs about women in leadership I am sure online we have this is my personal my baby because this is something I feel very vested into to facilitate the career progression of women and help them to become successful leaders so we have a website you may want to take a picture of this slide we have twitter account we have youtube we are on linkedin then on the whatsapp we have subject specific groups if you are interested in education our education group join if you are interested in agriculture we have a group for agriculture if you are interested in gender equality there is a group for that also there are many ways to stay in touch with us so please do feel free to stay in touch with us any questions so far any comments any questions because this is the first thing done any comments it doesn't need to be a question it can be a comment any comment you want to share thank you so much I am Dr Usma Hanif from government college university Lahore I just want to know how I will add myself in whatsapp group regarding the environment so can you elaborate this if you go to the website www.upsign.org.uk you will find links that click here to join this group click here to join this group the easiest way is to go on the website and click on the links to join subject specific groups is that okay thank you so much thank you Usma thank you very much okay so this is done this was the first part of my conversation with you today we will now move on to part number two which is critical appraisal skills for which we are all gathered here so before I even go further I would like to ask you when I say critical appraisal skills what comes to your mind who will be brave enough to tell us what I feel from the critical appraisal skill I think you need to identify some critical point and you need to tell them in some way that it is encouraging it is an appraisal correct I am not wrong so critique in a better way absolutely critique in a better way absolutely somebody else good afternoon hello Madina how are you nice to hear from you nice to hear from you nice to hear from you what do you think critical appraisal skills are I believe critical appraisal skills would be it would be something in which you are giving feedback keeping in view the pros and cons of the analysis which is student with respect to if you are talking about a student so we would be critically analyzing the assessment of that student and cons and then giving the feedback of how she can improve on it exactly absolutely you are absolutely right I think it is important to remember that as many people are connected am I right in thinking that you are all teaching undergraduate students if yes just raise your hand are you all teaching undergraduate students or postgraduate students for that matter or any university students so the conversation today is actually directed at giving these skills to undergraduate postgraduate students not a problem the two examples we have heard they are absolutely right critical appraisal skills are to give your critique or to evaluate something and let's take a very quick example who did not eat who did not eat let's critically appraise the beryani the first critical appraisal is that we do not have to praise that if it is good please praise it tell us what was good in beryani who will tell us what was the good thing about beryani sir you have eaten please tell us something how was the lunch what was the good thing about the lunch beryani was spicy that was good and the kebab I got a little less spicy no I ate two but it was less spicy perfect ok so basically you have given a critical analysis of this lunch you have evaluated beryani somebody else wants to take a go how was the lunch how was beryani how was kebab critically analyse ok let me pick somebody then sir you are sitting on the front row number two how was the beryani I hope you had it Assalam o alikum Assalam o alikum sir beryani was ok ok is good ok is good enough fantastic ok is good enough ok is good enough ok is good enough ok is good enough ok I see evaluations excuse me sorry to interrupt I too would like to analyse please do the kebabs that were late they don't have good presentation They had put in the same bowl which had rice first I am hundred percent this is this is your critical system this is not only your job is not to do tariff your job is toид critically Did it fulfill your needs? Did it fulfill your taste buds? Whatever that was. So this is critical appraisal. Abhi humne ek minute, doh minute ki andar-andar jo aaj ka lunch service thi usko humne critically evaluate kiya hai. Yani ki analytically humne usko critique thi apni. Is everyone with me so far? Okay. So this is in short words, yehi cheez critical appraisal hai. Ab biryani ka critical appraisal karna is a completely different thing. Or scientific paper ka critical appraisal karna it is a completely different thing. But the idea is the same that you are critically analytically assessing something. The critical appraisal skills, they enable you to systematically assess the trustworthiness, the relevance and the result of scientific papers, scientific studies. Kya wo trustworthi hai, kaunse source se aah rahe hai. Kya wo kisi unknown country ke kisi unknown publisher ne wo research studies wo publish kiye hai. Iska koi international ranking nahi hai. Uski relevance kya hai, uski results kya hai. How much you can trust a finding. How much you can trust a research study. How much you can trust the biryani, right? This is critical evaluation. Another definition of critical appraisal skills. Systematic process to identify the strengths and weaknesses of a research article in order to assess the usefulness and validity of the research findings. Jese abhi humne biryani ki strengths or weaknesses humne point out ki kisi ke liye uska spiciness thi wo it was a strength. Horsakta hai kisi aur ke liye wo uski weakness wo. Isi tahan ek research article ki jo humne strengths or weaknesses to analyse karne hai. So that we can assess its usefulness. That is critical appraisal skills. And it is an essential part of putting theory into practice because learning critical appraisal skills for your undergraduate students it allows you to determine whether findings should influence your decision making and it closes the gap between research and practice. Jo aap ne jo ek paper par rahe hai. I am sure agar abhi nahi aap ke bachhe par rahe hai to very soon they will start reading academic papers, they will start reading research studies. So what you have to teach them as their teachers is how to critically appraise a scientific study, how to critically analyse the findings of a research study. Why do we need critical appraisal skills? Kya zaroorata iss ki? Iske bagar bhi to kaam ho sakta hai? Why do you think? And actually let me unshare my, because there are some questions coming here as well. Oh okay, so how to join WhatsApp group, feedback. It's something like feedback on work. Fantastic. Yes. Jo log online. Sorry, I've just seen your comments now. That's absolutely fine. So tell me why do we need critical appraisal skills for improvement? Yes, correct. Jo auditorium me meri kolleeks bathe hume hai. Please do tell me why do we need, kya zaroorata iss sare janjat ki kya zaroorata? Because we want to move onward for the future. We want to move onward for the future, correct? Yes, someone else? To uncover the hidden aspects of the research which were not covered in that specific paper. Absolutely. To uncover the things that were not there jo ke, jo ke research me cover nahi hui. Ji, aapataye? To identify the gaps of the research and their improvement. Absolutely. To identify the gaps and to figure out ki yeh, is it needy? Is it trustworthy? Is the research even genuine? Jaise misaal ke torpe aap doktor ke paas jathe hain. Aap unse, aap jab doctor ke, aap apni koshish karte hain ki bhehtereen se bhehtereen doctor ke paas jayan. Jo aap afford kar sakte hain. Aap ko kyaise pata chalega ki that doctor is genuine and trustworthy? You will do your research. Aap kisi se puchhenge aage piche. Aap ko shat hui kahega nahi. I know that that doctor is a very competent doctor. So you want to establish the trustworthiness, the reliability of that doctor. And sorry, there are just some comments here in the question answer. For research and development, for future suggestions. Yes. And I'm going to show you this slide. Yeh batayein ke abhi COVID-19 jo hain wo ek talk of the town hain. Ham sab esteez mesi guza rahein kathe. Aap kisi se puchhenge aap doktor ke paas jayan. Aap kisi se puchhenge aap doktor ke paas jayan. Yeh aap jo slide pe dekhne hain. Aap ko yeh hain breaking COVID-19 coronavirus news. The second hain. It is about can garlic, can eating garlic help to prevent the infections? This is just an example ke medicine mein. You get information from left-right centre. It is so important to establish ke yeh information kaha se hain hain. Iska source kya hain? Iski research study ke methods kya hain? Is it even valuable? Is it even true? Iski reliability kya hain? And this is why we need critical appraisal skills. So that whatever decision hosakta hain us research study ke basis pe aap ne aage ek aur research study kreate karne ho. Bale ke nagar aap ke paas wo basis thik nahi hain, to aap ki agli jo research study ka design hain wo impact hoga. This example is only to show you that we need critical appraisal skills to understand ke garlic khaane se, for example, COVID-19 se bacha jaa sakta hain hain? Bacha jaa sakta hain? Can you tell me? There is a suggestion because if we quote here about ginger, so we can have many evidences that because ginger is used in different decoctions which is commonly called as kahwa, which is definitely cure your cough, which clear your throat and definitely help in the recovery of the person from the COVID. Correct. Garlic, I have no idea. Exactly. Absolutely. I mean, korn korn se remedies COVID ke time piyana shuru ho gain thiin. Kisi ne bola ki aap adhra ka kahwa lelein. Kisi ne bola aap rose garlic hain. Kisi ne bola joain kuch karein. So from everywhere we were getting all of these suggestions ke ye karenge to COVID nahi hoga. Ye karenge to COVID nahi hoga. And this is why critical appraisal is so important. Ke we need to understand ke je joe information hain me di jaariye. Is it even reliable? Or what source it is coming from? We need to find the context in which our own research will take place. What has been done before jo aap ke bachche research karenge? Will that be original? Or will that be almost similar to or a copy of jo research pehle ho chughi hai? Can we use what they have learnt in their study? Instead of reinventing the wheel, critical appraisal skills aap jab use karte hain, to aap ko apni study ka context milta hai. Apne, jo aap ke jo students hain jab aap anko sikharein hain, wo jab apni research study karenge, they can find their own context. Can we improve upon the methodology? Can we replicate unimportant finding? What has been done before already? Basically, when we teach critical appraisal skills to students, we teach them to understand what has been done in that field previously, so that they don't end up replicating that. As humans, the second reason we need to do critical appraisal is because as humans, we all have a trusting nature. Hamari hum sab ki jo nature hoti hai by default, hum bohot trusting hoti hain. We believe what we read in newspapers, hum jo TV pe khabre sunte hain, hum usko bhi kheen kar lete hain. I remember my mother she always says ke jab me khabre sunte hum to lagta hain, itni mulko kaum pe muskil vakt aagya hain ke shayat kal ka din aana hi nahi hain. But that is where the critical appraisal skills come in ke kaun see information hum ne on board leni hain aur kaun see information we have to path. So what we read in reputable journals and articles, we have to be more critical and more analytical in our approach. We also need to appreciate the good research, the good stuff when we see it, hum ek jo humare colleague bheti me hain, unko spicy biryani achi lagi thi. So you know, you appreciate the good stuff that you see and you critically evaluate the stuff that you are not sure about. Critical appraisal, it allows us to reduce information overload by eliminating weak studies, jo ke aap ke hain krat hi aya meet nahin karthi. Critical appraisal allows you to identify the most relevant papers. You can distinguish evidence from opinions, jo fact-based information hain aur jo kisi ka opinion hain, uske bhi chme hume distinguish karne ke liye critical appraisal skills chahiye. We can assess the validity of the study, uski jo strength thi wo kitni thi, uska sample size kitna tha, uski jo findings hain wo kis hattak implify ki jask thi hain on big populations. Critical appraisal skills, particularly, they help to assess the usefulness and the clinical applicability of a study, particularly in life sciences. Jo jo biochem ke log hi hain bhet hi wo hain. And critical appraisal allows us to recognize any potential for bias. By bias, I mean wo research findings that favor a specific group of people. For example, hain hain hain hain hain hain hain hain. To automatically assume kar liye jaayega ke they are not that capable of performing a task without even asking them, without even consulting them. Aur chote-chote every day tasks, e koi meh massive tizon ki baat nahin kari. But when we look at it critically, when we hold our judgments in check, aga horuks ko hum ek bilkul un-biased positions ek critically evaluate karein. That means that we can recognize ke hain hain jo biased hain, jo hain pre-judgements hain wo kahaan pe hain hain. I'll quickly look at the question and answers here. Future suggestions, immunity, et cetera. Okay. So we have figured out ke hain meh critical appraisal skills kyu cha hain hain. Aur hain meh wo kyaise help karthe hain. I do want to say ke it's really hard to talk about critical appraisal skills in an online workshop like for like one hour, two hour. But it is only, imagine it is a tip of an iceberg and we are only discussing this for the benefit of your understanding. How you take that into classrooms, that is a separate conversation. How do we do critical appraisal skills? We start with defining our research. Then we do the relevant searches, the relevant papers hain. Then we appraise them or we analyze them and then we evaluate them. The common questions to ask is the study question relevant to my field? Does the study add anything new to the evidence that already exists in my field? What type of research question is being asked? What is the study design? It is appropriate for the research question. Is it a qualitative study? Is it a quantitative study? Is it a mixed methods approach? Did the methodology address important potential sources of bias? Like I gave you an example, does the study even address that? And then talking about finding the papers that you want to read, you start off with doing a literature search. We use the web, internet web, we use PubMed, web of knowledge, coach train database, depending on the field, we have chemists here, some are biologists, I think some are clinical people. It's important to understand that the online tools you use to find research studies are those web tools that you are using for the literature search. After that, you generate a search by deciding the questions you want to ask. You use keywords, you use the criteria, you use the limits for example, not more than 50 years old, not less than 30 years old, etc. And I think it's important to remember that when you are finding the papers you want to reach, you will enter one keyword in Google. There will be hundreds of titles that will come back to your Google search. Then you have to start refining those search terms with tighter questions, limit your criteria. Just go through, skim through the titles and exclude the irrelevant titles that don't relate to your research study. That don't relate to your students' research study. Quickly read through the abstracts. I think a good teacher will always know that you don't have to read the entire four-page article. You can quickly read the abstract and you can figure out whether it will be useful for your student or your study. You can start reading and if it is not relevant you can just exclude it. And this is also, by the way, we will talk about that in a minute. It's also highlighting the importance of writing a good title and an abstract, which is a part of academic writing. So basically finding the papers you actually want to read just by your research study, your student research study, basically, that is really important. And I think when you teach a critical approach to your students, teach them how to save their searches, whether they are downloading them, we are noting the citations, whether they are making notes, whether they are using software, whatever they are using, teach them how to get to the papers they actually want to read. So the first step is done, we have identified the papers, which papers to read and we have to critically analyze them and then they will be useful for our own research study. Now we move on to appraising a paper, evaluating a paper. And I think really important to start with the basics as a colleague had said that Kabab was in the same dish and their presentation was not correct. They were in the same dish as the rice. So literally first impressions are the sections correct? Are there any grammatical errors? Are there any spelling errors? Usually a research article has a format, it starts with an introduction or a background and it moves on to methods or setting or the materials used. Then there are results, then there is a discussion and then there is a conclusion or the implications. So check that are all these things in place in order. If yes, it's a good start. Is the presentation good? Is it easy to read? Is it a flowing article, good prose, appropriate tone, logical flow? Are there any subsections if needed? Does it tell the story of the study? What is the house style? Are there lines on the tables, etc? Tables and figures are a really easy way to critically analyze a paper. Are they clearly labeled? Do you understand them? Or are they difficult to follow? And then usually there's a list of sort of critical appraisal questions that we ask. The first one is is the question relevant to your own research study? And when I say your own, I mean the research study that your student is doing. So is the question relevant to the study that your student is doing? Does the study add anything new to that? What type of research question is being asked? Is the study design appropriate for the question? Or is it not? Did the study methods then address the most important biases? Or is it an unbiased, non-judgmental approach? Was the study carried out as plan? Or were there any challenges they face? Were there any serious challenges? How did they overcome or respond to those challenges? Normally recruitment may be seen as a lot of challenges when it comes to recruiting participants for studies. Does the study test the stated hypotheses? If yes, what is the finding? And if no, what is the finding? Were the stats correct? Does the data justify the conclusions? Are there any conflicts of interest? Are there any sort of shared liabilities somewhere? So these questions are really important to consider when you are teaching your students to critically appraise a scientific study or a scientific paper. And then when you are writing a critical review, I think you have to remember to be fair. It's not only about giving praise all the time. It is not only about saying yes or being positive all the time. It has to be fair, it has to highlight the positives, it has to highlight the negatives. You have to provide a balanced critique, a balanced evaluation. And whatever you say, make sure your comments are defensible. I think one of you said the Biryani was okay. So okay is a very hard comment to defend. Either you like it or it's very spicy or it's not spicy or you don't like it, it was very bland. So you have to be fair to provide defence for your comments or whatever opinions you are making on that critical review. And then don't forget to consider the wider circumstances of scientific progression. How does the study that you are appraising and your own recent study, how does that contribute to the wider circumstances of scientific progress. And I appreciate that you may feel they probably are not that relevant to you or to your students. But you have to remember that for the purpose of today's conversation, this is what we are here for. And these are some of the basic scientific research skills that we have to teach our students so that they can be on the same level as a global platform at an international platform. And I am sure that many of you will be starting with students if the students are new probably. There will be some people who are in their final years who have degree. But these academic skills, these critical reviews are so important. So important, particularly at the next stage of the students careers when they enter the scientific world, when they want to work with international collaborators, when they want to work on international platforms, it is so important to remember that these are critical evaluation, academic writing, referencing, plagiarism, they are really important. So if you want to take away one thing from the critical appraisal, remember the Biryani example. It is absolutely one concept that you are critically analyzing any given research study. You have to figure out is it trustworthy? You have to look at different criteria. You have to figure out is it relevant and useful for your own use? And you have to figure out if it is going to help you with your own research. This is the end of critical appraisal skills. I want to open the floor for comments and questions and suggestions and I will quickly look at this here. No new questions. For how many of you, this is a completely new concept. Critical appraisal skills. Yes, doctor. The question is that critical review, critical appraises depend on the personality. Personality of who? The comment. The person who is doing the critical appraisal. Yes. It depends on the like and dislike. And what is the criteria to judge it? Either my critical review is okay or not. Exactly. For example, I don't like Briani. And some other person like very much. Some person doesn't matter that it is very well presented. For me, it is very well presented but I don't like it. You don't like it. Absolutely. If the Briani is much spicy. And he likes spice but presentation is not good. So how you will You're absolutely right. Critical appraisal is a very beautiful thing that it is very individual. Every individual takes it. You don't like Briani. The person sitting on your left maybe they like Briani. And this is why you have to understand that there are set criteria, there are set ways to assess the paper. It doesn't matter if you like the subject or the topic. What matters is whether it is reliable or not. So for example, what we are talking about of garlic and ginger. It doesn't matter what you think that they have a COVID cure or not. What matters is where this information comes from. Is it only a grape wine that what do you call it without any evidence is it like that or is it coming from a scientifically proven study. That is what is important. So it is so important to keep your biases on one side when you critically appraise a paper and understand the positives and negatives of a paper. So personally you might not like Briani but that doesn't mean that they are not critically appraise the Briani and let me give you an example. Food critics who work for restaurants I don't think they like all the dishes in the world but their job is not to like a dish. Their job is to critically keep presentation. If there is a ghost, what is the spices level how is the texture how is the composure Keeping in mind that if you have a personal preference that should not interfere with the judgment of the Briani and I know it's really hard to get that it's really difficult to achieve that particularly this conversation to achieve it in one setting but if you want to just remember one thing that is important to remember that critical appraisal means being fair, being unbiased in providing your critique I don't know if it helps or not this is something to think about in the wider context of scientific papers and scientific research Any other comments or questions please I would be very interested to know what is the level of research methods or scientific research that you teach to your students Can somebody share it please Good afternoon Can I ask a question Okay When usually students come to this point when they have to analyze or they have to read the research papers before that they usually adopt it with the textbooks like whatever they are reading it is true sometimes it's very difficult to understand or to get them to path that okay for textbooks what you have read is okay but when you are studying a research paper the knowledge available on that basis they come from different sources they cannot be so can you put some suggestions on this how we can make the students understand this point Absolutely and I think Yuri is a very important point that the simple answer is you have to make your students researchers you have to make your students into independent thinkers the scientific query the intrinsic questioning ability you have to encourage them the book the students have read it the textbook we have also read it but that is the problem that if a student cannot question or they don't know how to question the scientific paper that is what where critical appraisal comes in and whatever you have said exactly we teach our students don't trust everything you read on the internet similarly we have to teach students if you are googling something about cancer for example if you have written a word cancer screening you are going to receive millions and millions of results this is how when you write a word where on earth will you begin from from where will you start nobody has the time to go through millions and millions of those results so there has to be a way in which you can choose the reliable studies you can choose the valid studies and that is why critical appraisal this is what critical appraisal is enabling you to do it is teaching you which studies you have to discard which academic paper and which paper is not useful and again going back to this slide the starting point is finding the tell them how to teach them how to find the paper how to reach that data whether you have to use any web or use any other databases this is where you have to teach them how to be critical when they approach limitless information on the internet and once because you have to make them independent thinkers you have to give them the scientific inquiry and once they get that paper even from that you have to refine use tighter questions extract it is like a funnel top down approach refining to this much of of questions and information I don't know if this is helpful but I have tried to respond to your question yes thank you so much thank you I want to ask you what kind of research skills what level of research methods they have what kind of research skills what level of research methods they have can somebody please share with me for example do students know about qualitative and quantitative research methods they do ok fantastic when we talk about qualitative can somebody tell me please and I totally appreciate that there are different varieties of people from different places I am very interested to know because it means different things for different people what sorts of qualitative methods are taught to your students can somebody share please I think I have asked a very difficult question we have a pharmacy practice a subject like University College in London in the name of social pharmacy we do projects like the current situation of COVID so I was doing a project in which the effect of COVID and menstrual cycle in different age groups for that scientifically in the pharmacy there is some software available that analyze the data qualitatively and we input their different modes and their names for example we use a pharmacy practice to evaluate the data clinically its name is Stepple it is available we download it or purchase it ok so basically this is sort of specific to pharmacy for that specific field thank you I am just figuring out the qualitative methods who of you actually teach students Amitya all the biosciences use this quantitative method ok so more quantitative fantastic lovely we all love numbers ok we are all numbers so I am guessing that you are all smart because when we talk about quantitative we are talking maths this is how it is so do students know about different statistical tests do they know about chi-square for example they are taught at the undergrad level ok ok ANOVA ANCOVA do they know about that as well ok fantastic lovely so you are already telling me that your students they are already aware of scientific approaches if they are at the undergrad so this is where also they will become independent thinkers they will become researchers they will become scientists and this is where all of these skills, critical evaluation academic writing, referencing they will all start coming in is there another comment I want to share one thing yes ma'am in undergrad level we used to teach them about how to use referencing softwares with some software like graph pad and SPSS and different type of referencing software the people are using this similarly for the bioinformatics the students are also using different tools for their research so basically I suppose the software that is mostly SPSS that you are using for kids SPSS and graph pad prism is somebody using R by any chance okay so I think SPSS and graphics are used so I think we have to remember that the software is a different thing and the research method is probably a different thing they are both intertwined and I think let's just continue with the understanding that when you are working with your kids you are helping them become scientists and this is where their critical thinking has to check in because as scientists this is a question this is their job to question and analyze so I will end this section 2 here which is about critical skills in the end there will be more time for questions and answers for your comments I will quickly glance here Phenomenological oh my god I can't even say the name but whatever that is it's fine I think what you are saying very cool thank you let's move to section number 3 which is the academic writing skills you all are sitting here on call this is a critical critical the most important skill for anyone who is studying life sciences biosciences, medical sciences I think when I was a student many years ago I didn't have any academic writing skills at that time one of the skills I had which was taught in my college that was copy and then paste and maybe some of you can relate this to but there was no concept of academic writing there was no concept of referencing back in those days time has moved on there are many things worldwide in Pakistan in UK things have moved the critical thinking the inquiry based learning the academic writing and I am so happy to see that because the biggest shock when I started my studies here in UK it was this that I didn't know academic writing I had no idea I had good English but it was not academic academic writing is completely different to English writing so if you are here today if you are listening to this conversation I would ask you if there is one thing you take from today please do give your students the academic writing skills because most of our students come here and eat you give them math questions they will solve them you give them in an interview they will do amazing when you ask them to do an academic essay that is where they struggle and I say this after 12 years of experience of working with international students when our students struggle in international universities this is the first step this is the first hurdle the session starts in October normally the first assignment by November they have given up hope excuse me by November they have literally given up hope that I don't know academic writing I don't know where to start from I don't know how to do proper referencing I don't know anything about plagiarism etc etc etc so if you are in a position Allah has sent you that you are giving knowledge to your students give them the skills of academic writing and what we will try literally in a 1-1.5 hour conversation it is very difficult to cover these skills because these are full-fledged workshops as I am sure you will know but what we can just do is we can go through these next few slides together literally as a refresher so that the points in your mind refresh and then you can take those back to your students are we ready give me a thumbs up please if you are ready fantastic thank you and those who are listening online give me a thumbs up so basically academic writing structuring the essays and research papers how to structure the argument the writing process and then developing an effective writing style and avoiding plagiarism very quick overview when we talk about the structure we talk about structure of essays when we give kids assignment to write an academic essay this is the question or title now write an essay or 3000 words critical appraisal which is by the way also an academic writing element so what is the structure the structure of the essay is to outline and develop a preconceived coherent argument not left right center it has to be coherent it has to flow through it has to persuade the reader of the value of that argument whatever the argument even though the argument is that Covid gets better but the essay should be so that the reader should be convinced and then why is it more powerful than potential competing arguments that your essay argument is why should somebody believe that so basically we start with such questions usually what is the essay question asking you to do analyze the question basically three components there is a task word what you are required to do with the material then there are some content words what content should you be drawing on what method what research you should be using and then there are D limiters what are the limits of the content that you need to draw on and I'll give you an example and it would be great to interact with you think of this essay title critically evaluate the usefulness of motivational theories for understanding preventive health behavior now those who are listening online and those who are sitting in the stadium can you tell me what are the task words remember the task words are what you are required to do with the material you can shout out the answers or people who are online you can type in the answers what is the task word in this question yes critically evaluate that is the task word which is telling you what to do what is the content word and the content word for your reminder it is what content you should be drawing on understanding the motivational theories this is your content on which you have to go you don't have to go towards the recipe for making biryani you don't have to go towards how to plant trees in my garden you don't have to go towards how to fix a puncture in my tire the content word is motivational theories this is the content which you have to critically evaluate and then what are the D limiters and for your reminder D limiters what are the limits of the content that you need to draw on preventive health behavior the task word you have to critically evaluate what you have to critically evaluate motivational theories what is the D limit how to justify it preventive health behaviors so I think it is so important that when you are setting questions for your students or when you are giving them that information take some time to set the question in a way that it has these three components in it it could be anything in biosciences in your pharmacy you should contain these three things because remember keep reminding yourself that you are helping your students to become scientists you are helping them to become academic writers, independent thinkers so when you have pinned down the essay question help your students to develop the essay plan normally you start with an introduction about 10% of the word count in the introduction you acknowledge and contextualize the question you contextualize the question for example I will give you a very easy example the universal truth is chips khane se mutapa hotay we all agree on that if somebody disagrees they can tell me now and then we can talk about that does somebody disagree with that so chips khane se mutapa hotay but how many times can we frame this question in a different way can we say for example how much chips khane se mutapa hotay is 9 years to 14 years or can we say that people who have existing heart conditions how chips khane se mutapa hotay so whatever the context is whatever the essay question is we have to contextualize that and in the introduction section we give an overview of the structure of our argument then we move on to the body of the essay which is about 80 to 85% of the word count we develop our argument whether we are doing the critical review whether we are doing the literature review we synthesize the evidence to support our argument and then the final bit is the conclusion which is about 5 to 10% of the word count we sort of draw together the main points of the argument and to conclude that the view point is valid or indeed not whatever the essay question is then the writing process starts now the writing process and again I will totally acknowledge that an hour 40 minutes is not enough this is a full-fledged half-day workshop on the writing process right now what we can just about manage to do is we can skim through these things as a refresher for you so that when you teach these things to your students you are well equipped we start from pre-writing you just make some main notes, main points then you plan, you do the essay structure then you draft it then reflecting and revisiting keeping, making changes then editing and proofreading and then completion or the submission of the essay and the writing style the writing style has to be really effective writing style it has to be formal because an academic article is always a formal article it has to be economical by economical I mean in terms of the word count because you all know that when we submit papers in international journals there is a very strict word count we can't go from here to there we can't go from there this is one of the skills we all struggle with how to be economical with words the writing has to be clear it has to be simple use jargons not try to bombard the reader with too many complexities it has to be assertive if the academic essay if he doesn't believe his own argument then they cannot convince the reader it has to be confident and it has to flow at an appropriate pace you cannot jump from introduction to discussion and then jump back to theory it has to flow at a pace that is already planned out at the planning stage very quickly let's talk about plagiarism some of you mentioned that this is one of the things it's such a big risk that the academic we write plagiarism by accident we end up by accident with ideas and very quickly what is plagiarism can somebody quickly tell me I'm sure you all know this maybe I don't need to ask you it is literally quoting someone's work or presenting somebody else's ideas without acknowledging their efforts at their time and this can be done accidentally as well in academic circles it is a serious offence academic dishonesty and it is called the presentation of another person's thoughts or words or artifacts or images or songs as though they were your own yeah again very quickly copying words or ideas from someone else without giving credit and it is as easy as failing to put a quotation in the quotation marks I think I know a student he had a quote but on that quote he forgot to put commas and because of the quotation marks he didn't get that counter test plagiarism and they were penalized for it and I think plagiarism is also when basically it is the same concept but we are just changing words of a source without giving them the credit and our students this is a very very common mistake to make and then talking about paraphrasing and referencing this is so important to teach our students that they are used to paraphrasing or referencing styles the simplest way to avoid plagiarism is to paraphrase and reference all the sources make notes in their own words when they are reading articles and then once you've done you've read an article move the original source out of sight and try to summarize the findings in your own words because then it means that you are actually reflecting on what you learned not copying the article over word by word of course there is always a question should I paraphrase or should I quote so putting in your own words that is called paraphrasing if you have read an article then you try and come back and write about it again that is paraphrasing you are putting it in your own words which is the best practice one level another one which is the acceptable practices using direct quotes from the research paper within quotation marks and using the appropriate citation which is an acceptable practice it's good of course it uses up a lot of word count by the way and the worst and the unacceptable practices that students are using direct quotes without quotation marks without citation which is exactly what plagiarism is as I gave you an example that the student named a complete quote from a research paper without putting the quotation marks and this could happen very easily by accident but this is plagiarism and I am sure you are all familiar with self plagiarism as well sometimes we refer to our previous work without making a note of it that is very easily done self plagiarism so be mindful and teach your students that if they are referring to a previous essay or if they have done something they are also giving citation for that Effective writing this is the last slide I promise you effecting writing is a key skill this is a very important skill for healthcare professionals if you are not a healthcare professional you are in biochem you are mostly in life sciences people sitting here for anybody in life sciences effective writing is an absolutely critical skill it's not only about writing planning, drafting, reflecting proofreading it is more than that it is about building a coherent argument and what you must teach your students is that the time they will spend in planning their article or planning their research study or planning their essay that is time well spent the style that they want to take that is a skill that will develop over time it will be nurtured it will improve over time they can consult textbooks there is so much information on the website on the internet it is a plethora everyone is free to google different Harvard writing style APA writing style, in house writing style whatever that would mean the referencing and the writing style is what will actually protect you or by you I mean your students from plagiarism so I totally appreciate that it is really hard to encompass everything about effective academic writing in one conversation like this but I don't want to over burden you with information I don't want to over burden you with too many slides too many text words if there is one slide that I would ask you to think about is it is this slide please do pay attention to this do teach your students how to structure their essays how to do academic writing and I think normally my daughter she does this very often she wants to start writing an essay and she wants to get it right the first time the first time she writes there is no grammatical error there is no argument error there is no spelling mistake I think this is a common error that we all make we forget the drafting part we forget the planning that needs to go into academic writing and we jump straight on to writing a perfect essay the very first time so if you are teaching your students the writing process if you are teaching them how to do academic writing teach them how to plan teach them how to build a draft teach them how to go through the draft again and again edited proofread it until they reach a point where they feel they are very happy so I will I think this is it I will again quickly recap we have just done academic writing we have done critical appraisal I want to ask you now my two questions to you are what are the most common challenges that you face in teaching students, supervising students working with them and particularly within life sciences or within biological sciences and this is the same question for many people who are online the second question is again this is for maybe for virtual university to take up what do you think will help you what sorts of trainings or what sorts of interventions will help you as a teacher so that you can better deliver your lesson plans over to you please I will stop the screen share now because I would really like to hear from you Ji please who would like to take the the most challenging thing in supervising students is that they've got a very weak language expression so although they've got really marked out concepts in their brains but they are not able to put it down in words so probably that takes almost a whole year or semester for them to have to come up with a perfect draft or probably more than a year as well because the English expression the correction needs to be done at the grass root school and higher secondary level at the level of undergraduates we cannot really do much in six months semester I totally appreciate our schools should work on English expression you are absolutely right and I think this is I mean if there is one thing the most important thing is that the power of writing they struggle with that that is unfortunately that is the one thing where kids are a little bit disadvantaged like I was saying they will do it when it comes to actually writing a coherent argument that is where they struggle and you are right this goes back to school and college 10 years in school and 2 years in college or 3 years in college so you expect as an undergraduate teacher that when they come to university they will already have those skills and this is what we have gathered today when they come to university not all of them have those skills and again I wish I had a magic solution for that I think I don't know that in your modules usually the first the first year in undergrad there is an entire module dedicated to teaching academic writing in which they are taught how to build an argument literally starting from basics they are taught critical thinking how to question how to accept everything just like without questioning the validity but you have to question it and ask any question like we have seen in critical appraisal slides and they are taught how to plan how to write dedicated to teaching writing to students here in the UK Ma'am, what are you saying? I want to add some comment regarding this language barrier basically because our students in homes and schools the basic medium of communication it is Urdu and if we give some return to them in Urdu they give a very critical design they want to ask you anything they will tell you if we change the language for them it is an alien language whatever you try you must have seen I have a objection to my education system we are not working for giving them information we teach them language for 10 or 12 years we teach them language 100% I share your frustration when we keep them then how do we expect they could be a good critical thinker they will only use language they will say what happened in the past how to use the present and future tense how to use the relative degree that is it which we have never remembered in our life Nighat is also writing this comment they don't have basic writing skills and to make them understand the basic writing skills in a virtual system if it is difficult to teach them in real world then we will forget I share the same frustration I am on board with you I am a victim of that when I was a student I used to write like this but I didn't know I was fortunate I went to convent school I got 1-2 words but when I was shocked my system when I came to UK I understood from my side I would be the best student when I started my masters and I was horrified to realize what happened I don't know what I have to write I can write a newspaper article I can write I can write I can write a letter to my husband I can do all of those I can write an email but where that academic writing comes from language is such an important issue and like I said crying for this or finding a solution and I think what I can say is that in one setting we cannot disrupt this system we are in a 2-hour conversation these are not things these are systematic changes these are policy changes these are the responsibilities of the government these are the responsibilities of the educational institutions I think what we can do in our individual capacity is the same as teachers and teachers are the same the way you are the way you are the builders I think what we can do in our individual capacity is that what we can learn in our capacity in the same constraints I support you 100% the issue of language the predominant language in homes is Urdu it is not taught in schools in the sense how to build a structure it is hard on grammar we have to work in these constraints in my life most likely there will be no change but we hope for a better future I hope somehow you have improved but we will work together as long as we are alive I think your 7 colleagues were raised was that here somebody else please you are a very good presenter thank you and it was great hearing you I will tell you one thing Pakistanis in medical sciences in engineering in toppers all over the world when the U.K. and America had a selection our doctors were in the first positions our engineers when they were in U.T from a college I am talking about the 50s like this at the college there were toppers and there was no challenge they did not have any challenge it means there was no barrier language there is one thing of Einstein if you can understand a thing in a simple way then you can describe it true and when you can describe it it means correct our scientists at that time they really used to input basically to explain I did not do you know the square of 14 to 40 is 800 one of my teacher told me if you want to do 40 to 40 then do a square plus b square plus 2 a now you can apply this formula take the whole square of 45 you will get the answer 16, 16, 5, 5, 10 ma'am do not ask this question no I am just joking what did our students do they instead of simplifying they went to the passive remember what is written without understanding the basics without understanding without putting into it I had a college graduate and he used to write so beautifully English at that time he did not have a computer at that time you can see the csp at that time this gap is in our struggle this gap is in our struggle my the most painful thing about my students I tell them what is the purpose of your life what is the purpose why you are a human being and you are a female all of this is for the upper class what what is the next what is ahead similarly when you are reading English literature or scientific find the crust what is the main message what is the main message what is it if you know the main message and you tell it in any language it does not matter 100% you are absolutely right I think what I want to add is I feel in many ways for teachers people like you there is so much of work pressure to complete the syllabus work on work it is a two way street children are getting lazy they want a cooked halwa we are getting information we are not getting knowledge we are not getting knowledge it is an argument and that argument is so true and it is happening in the scientific one student tells the other student you know I have read the Falaam paper without seeing it is so strong I will find it he listens to his friends and downloads the same paper he downloads it he publishes it you are right I think it is a personal responsibility a woman who is trying to find a partner for half an hour a boy who is trying to find a partner wherever he is he can find a partner the same girl and the same boy why can't you read the article from different places I agree you are right I totally agree I feel the responsibility it is on both sides I think probably more so on students as you mentioned when we were students which computer was there which google was there we all went to the library I understand that was a different time and now is a different time and the call of Hazrat Ali to increase his time because he was born for that time so I totally see that there is some onus some responsibility on the students how much we will spend and if we keep spending then the post grad level the PST level they will need a solution and at the same time the onus is on teachers as all of you in your personal capacity the same constraints as much as you can extend your knowledge all the resources today you all have attended this conversation this is one way this is a two way traffic it is going to continue like this or wishful thinking wishful thinking and everyone has critical thinking skills everyone can make a baryani academic writing we can just think and hope for that but thank you for your input ma'am please do share with me I have one comment it is written she has said mostly what I encounter is that students trying to avoid plagiarism they break the entire structure of the sentence and they need a lot of training in paraphrasing and summarizing I don't know which one of you struggled with this paraphrasing please can somebody move that to see everybody ma'am, do you have a question? I would like to add I think the first problem that students encounter is that the difference of approach in study they have different approach they think we have to read and the exam will come from that when they come to the practical or when they come to the research there is a different approach you will give time you will get involved in this and you have to approach not only when you have studied but you have to do critical thinking you have to broaden up your vision so the first approach is the difference I think there must be a course or something that we have to research and teach the kids how they will develop totally agree ma'am what you are saying is how to apply the critical knowledge because if you buy a question from the right the question comes out of syllabus right? most of you have to define that you don't have to read and absorb it you have to ask you have to do it and you have to go ahead in the textbook but for research to do something else you have to go ahead you have to approach and that is exactly the scientific enquiry which we have to teach our kids as ma'am said if the student comes there to look for a mobile for hours to study after 2 hours they don't have mobile they sometimes check on facebook sometimes on instagram there are so many distractions so I do feel sometimes the input from them that needs to be further pushed we need to do more if our kids have to compete on the international platform if they pass a bare minimum degree that is it that is different but if they have to become international scientists if they have to become international thinkers they have to become questioners and that is the difference it is about teaching I am guessing that the final year there is a research project mostly in universities so before the final year every semester every now and then some training workshop that is so important I can now see some male colleagues I have not heard from them at all it would be nice to hear something from you please okay now I will pick so I will close my eyes and I will say please share your thoughts with us please mic them go thank you sir you were here did you attend the whole session yes I have attended tell me sir please what do you think I would be really interested to hear what is your experience what are your challenges what is it like for you being a teacher and from background of academics I really think that there is a diversity in students there is a lot of diversity I was talking about that in this era students are not so responsible but I have seen that there is an immense population pressure many students have good knowledge and one of the recent news I have heard that a student from a college published an research article in Impact Factor Journal the thing is that we should improve some content in schools and in colleges and the universities but just about the thinking ability is different students are very good but some students need some special training we can make them capable I totally and in the end I will just say that your presentation was good we should conduct some training on plagiarism and paraphrasing in future I totally see that I think we must all acknowledge that where we have such kids who are lazy there are also such kids who are toppers who give them credit a critical rule of plagiarism is that give credit where credit is due if you have a good biryani then say that you have a good biryani so I think all the colleagues here I also saw the news of a very young kid who published a research article that is amazing because in our country there are very good ventures and there are a lot of like fight kids like you who help those kids so I think in the comment chat the plagiarism and paraphrasing those are critical skills as a bare minimum those skills should come at the undergraduate level my daughter is 17 when Covid was going on 2 years ago when the first lockdown was coming and we were all working from home when we are always together when you start getting into the face of each other you fight you get angry I was getting very annoyed my mother was doing my head she was 15 years old at that age so one day I thought I don't know how long I have to work from home even the house is small so I think I should just keep her busy I should give her a project that she should do her own work and let me do my work so I told her you are 15 years old you make a project how are you coping what are your opinions what are your worries what are your thoughts what are your studies what are your friends etc first she was very annoyed then I gave her money that I will give you a consultancy so you make this project of course then she agreed then she sat with her father she surveyed everyone it was this question then she ended up writing it as a report then she wrote research methods she wrote the main findings as if an academic article is written and then at the end I was so happy to see she had a reference list that I had read these articles so the point I made I am trying to make is that it is so important that we do this investment scientific inquiry which is an investment which is an investment to teach referencing which is to avoid plagiarism this is our time investment right now which will help our children in their work in 5-8 years so that research was really impressive then the University of Oxford approached now she sits on their panel as a youth advisor I don't know what she does but my point was that I had to invest time how do I use this effectively as a parent how should I engage her and that one thing I did for her that had really good implications for her she understood a bit of scientific writing which can save 15 years she got some money she was happy she understood referencing so she was really really into that she was one and a half hours into this conversation I do want to invite any other comments any other questions any other suggestions there is a question what percent of plagiarism is acceptable in academic writing so Mr. Vijayar academic writing you all know that there are softwares when a student submit we run it through a software that tells us that this part is plagiarized this part is plagiarized it should be highlighted you could be at 5% and still plagiarize or you could be at 35% and not plagiarize so it happens that if you are normally at an acceptable level 15-20% and below chances are there is less plagiarism or there is no plagiarism 15-20% international what we see on the platform is that people are more and more careful that it is going towards plagiarism I don't know if that answers your question Mr. Vijayar if it does then write in the chat but I do want to say it is an individual case like I said all it takes is one quotation without the commas and there you go plagiarism is done so if you are talking to a student put plagiarism in their thinking teach them the skills to do the referencing you have to write a reference that is it you have awarded plagiarism so any more questions my question was yes sir a ma'am said this in detail so I thought I should say it too yes sir please the attitude is an issue on both sides I will talk about the supervisor and the student the gap is the attitude for example if I am a supervisor then in 8 hours I don't have time I am busy and if I am a student then in 8 hours I am busy but I don't have time to discuss with me so it is on both sides and secondly if two children are living in a different house then you can't keep them in one line you can't say if you have published a paper then you should also do this there is a big difference in the environment and in the house then you are dealing with the supervisor so I will say the student's attitude is also an issue and the supervisor's attitude is also an issue the attitude in a sense that we don't have time and this if he studies for 12 years then it doesn't mean that he will come to you on the first day or the second day on the 30th day and he will tell you that he has read the paper I mean I don't remember in the FSE that I had any idea about this article I didn't have I have read the DNA but I had to read the paper the supervisor of BS he told us he told us he doesn't tell us tell us I am not saying it openly so these are some gaps all the things if I took 20-25 years to read the paper or to read the abstract then I want to teach my child to teach I will teach but what we are doing we are looking at what the child is doing and the child is looking at what he is doing and how I will hide and leave leave from him you are right it is kind of a two-way traffic and I think the one thing which is advantage for these children which we didn't have now these children can open google can open youtube and access a lot which we couldn't do even if it is a food recipe even if it is a critically appraisal even if it is a plagiarism so these children have the resources which we didn't have we used to have textbooks or we used to have teachers or we used to have libraries in a school in which we sometimes had less permission or we could have only two books and whatever that was so I think along there is a lot of revolution and the more responsibility it is for the children the more responsibility it is for us and one thing I would like to add is the responsibility of the institutions about your workload because that is a big constraint if you have time then you will be able to give it to your child but if you are being kept in administrative work or your workload allocation that is literally the attendance you will be able to read and your child will be able to read so again some institutional input some personal input some student input it is a biryani of everything it is a mixture of everything I think and from everyone as I said before probably the system will not change in our lifetime but what we can do in our individual capacities is to learn one or two good words that we can send to our children any other comment? I would like to comment please sir being a teacher what I feel is before blaming the student if I am a teacher then I need to think over I will explain some examples you have given an example of your daughter you might be saying you will know better you invested on her and now she is part of some duty belongs to Oxford I will give you an example I was listening to a story which was made by Bijlee it was her name her mother when she went to school to get her admitted she was taught a few lessons then the principal gave her a letter and told her to take her she is an extraordinary child when she came home she asked her mother why she took her she said she is an extraordinary child she said we do not have the capability to teach you I will teach you she did not have the strength time passed and the principal made Bijlee she went to her mother's room she opened the box she said she was right when she opened the letter she was mentally retarded she needs a special school we take her to a normal school her mother hid this from her she brought her home she lied to her she was an extraordinary child she wanted to teach her she invested on her she taught her she made Bijlee how much we invested on our students I remember when I went to school it happened two times she said her fees are that she will come regularly she will not leave if she leaves I will teach her she went to a teacher I remember when she used to come we used to hold her the same thing happened I told her fees are regular even today she bought me I invest how much I invest I don't invest how much I invest on my students my priorities are something else along with majrat being a teacher I am very tensed I have 5-6 papers this year because I want to go to philaj I have designed all schedule I am not concerned with my teacher if I am concerned with my students again with due apology how can I use this I can do better 100% this is reality this is reality we do so much I invest on my students I invest time on them like a coach we teach like a coach does to a sportsman like a mentor we watch everything we are very conscious we are very emotional we say okay if someone understand we can benefit mutual mutual is a mosaic we spend time with students if we have a good relationship otherwise how much we invest on weak students I remember that chapter if we forget then there is no point in which a child enters in English class in 12th class the whole chapter was taught in English book that is in English the entire year the whole year English is passed Don't anything happens remember the full stop after paper teacher calls a teacher like me he says that he wants to convey what he wants to do he calls he closes the chapter then he becomes a professor You can't expect this to be a long speech. I am answering it myself. Then the student-teacher ratio, you were counting international figures. I think if we are not wrong, the student-teacher ratio, according to international standards, one teacher can focus more on 20 students. You can focus properly. Yes. Not more than 20. In one class, 20 students will sit. Madam, they are sitting in front of me. 220. Sir, same. Same. These are some issues. Absolutely. We will not put students in. Absolutely. I am standing on the podium. He is sitting on the bench. I have a claim. I am more than you in knowledge. I have gone to the podium. I have put them on the bench. I have put them on the bench. They also say that leaders are the lead from the front. Being a teacher, we are also a leader. We were saying that we are the leaders. I will have to sit on my own. I will have to sit on my own. I will have to drink tea. I will have to sit on my own. I will have to sit on my own. I will have to sit on my own. I will have to sit on my own. Sir, 100% everything you said is fine. I think it is very insightful. It is very honest reflection. You are absolutely right. I have some infrastructure issues. For example, just to give you an idea... I saw in the UK that the teaching staff has to teach. They don't have to assess the base of the papers. They don't have to assess the funding. Research staff is different. So, of course, when we're talking about institutional change, because remember, don't be harsh on yourself too much as well. You're in your capacity, you're in your constraints, whatever you're doing, I think you're doing very well. So, your concerns are on both sides. I think we should put all of us on students, that's not right. We should do all of us ourselves, that is also not fair. I think, as I said earlier, I don't think there will be a system in our life that will be perfect, in which we will get allocated time for teaching, allocated time for research, for grant writing, for the funding proposal, we will get time for that. These are all the wider issues. I hope that the organizers in this position that they can consider these things, they can take these opportunities, Samar is sitting here, I hope she can take this feedback back to the people who make decisions. It is a lot about which resources are going and the mentoring, coaching, student well-being, that is really, really important. Because right now, it's not enough and as a teacher, would you invest your time in a student? When you have such a long workload, you have to publish your paper, you have to grant writing, etc., you have to mark it as such. These are very valid issues and they are complex, they are complicated. I think that by sitting in one setting, we cannot reach a solution. What we can do is, we can create these platforms where we can have conversations, safe spaces. And today's conversation, it is one of those safe spaces where we can share our frustrations and our achievements. And the people who are sitting on that position, on the power position, who are sitting in the authority, they can take these suggestions on board, they can take these ideas on board, they can incorporate some of them. So the purpose of today's conversation was to talk about academic writing and critical appraisal. Apart from that, you have to understand what your challenges are as a teacher or as a person who is imparting knowledge to you students. So we are 10 minutes away. I would like to draw this to a close. I would want to thank everybody who has participated today, shared their knowledge, shared their concerns. I'll quickly glance at the screen. I think there are the same conversations that are at the master's level, at the undergrad level, academic writing, plagiarism. These things should be inbuilt from the beginning so that when the students come to us, they are ready for the scientific inquiry. And of course, there are wider questions. There are wider questions about staff support, staff training. There are wider questions about staff teaching, work allocation, etc. Let's hope that these conversations, you know, we will continue these discussions. If there is something or the other, then you are doing fine. If there is something or the other, then you are doing fine. Again, I would want to end on that note that whatever you are doing in your capacity, wherever you are doing, whatever you are teaching the students, I salute you. In my view, you are here. So, may God give you the opportunity to continue this noble profession. And I hope that I have shared one or two words with you today. If you just take them away, think about them, and if you can pass on anything to your future students, then I will understand that a good thing has happened today. Anything else? Anything anyone wants to say? Anything else that we have to do today? I think we can all clap for each other. As much as I have learned from you, I would like to talk to you more and listen to your conversation. Samar, I will give you the final word from my side. A massive thank you and my best wishes for you. I hope that at some point you will meet the most in person, in some other training, in some other session. Over to you, Samar. Thank you so much, Madiha, for joining us and spending time for us. And I hope it was very engaging and very interactive and informative session with all our participants. And when you come to Pakistan, Nishana, we will plan some live session with you, Nishana. Thank you very much. Thank you so much. Definitely looking forward. Stay safe. Take care of yourself. Stay safe from COVID. And keep your scientific inquiry alive. Thank you so much. Thank you. Allah Hafiz. Thank you so much, participants. You can go now.