 Thank you very much for coming First thing that I would like to do is sharing my feelings Because this is my first tech conference and I am really a scare But at the same time I'm really excited to share with you what happened when a biologist met Python This biology is me I did a PhD molecular biology and after a while I was a science if stay in academia or go to industry And in this time I just start to learn Python because I knew that it was useful for science and And it was kind of I in this point I discovered I start to discover some models and packages that was kind of amazing in that point I Start to I don't know to have a kind of Relationship Wow, this is amazing. Why I didn't start to use it before this moment well, I decided to move to industry where I'm working as a Product data manager it comes platform that we sell products for scientists and One of my role was looking for new New Resources in this case publication and it was in that moment when I realized and I discovered some amazing tools But I thought why I cannot share with the wall this new discovery And that it's a why I am here today Well this this talk is not a conventional talk We are gonna have biological adventure But with Python that means that we are gonna cover some different biological topics and Hope Python can have a role in this As you can see will be really different stoppings My first story is about plants because plants are amazing. They are there and they cannot go They cannot speak but even that they can communicate one of each others Imagine the situation. We are in our living room We have a plan that is living there really happy and this plan Perceive or see the light with two different kind of waves But we saw um, it's amazing situation, but maybe I can buy a new plan and We sit there because my plan is really happy there I can't have a new one near and in this situation You arrive to your home to your living room you left your plan and the second plan also see the light to the same way but this plan also reflect a kind of wave Saying that the one plan can detect to another and they are Started to be unhappy because they are feeling that they are in danger They need to survive because they are in competition for life Amazing topic if this was my topic of disease and Imagine that you want to know about this syndrome that it's the generative for this situation That is called shade avoidant syndrome and This is where Python can help us. We can use this model called by a Python To look for more information in this case. It's a simple example Where I am looking in a database called PMC As you can see in the line 5 and also I am looking for them I choose this this database because contain open access publications But there are many other databases that you can look a lot of kind of information related with different fields and in science in general In the second part of the script we are doing a parsing of the information and Then what we are going to change in this case is title and URL, but Again, we can obtain piece of a text and other information And then we can see that this also has two different publications in open access journals, sorry Well, sorry, I did I give you an spoiler for the my next story But I wanted to say the last thing Remember if you have to plant really close at home give me give some space to them. They will be happier My next story is about avocado because avocado it's a fruit from all that Adam I don't know if you know that but this is the the the aspect that the primitive avocado was The the seed was huge and this was a really problematic issues because they It is really difficult for this person of this of this seat But Thanks to this animal. Well, not this to the grand-grand-grand parent, but it was a giant a slot around four meters of size That eight avocados We have avocados nowadays But you can think yeah, but this is an animal around four meters only avocado it's enough Well, it was not enough for this animal He needs to eat avocados and other fruits and for that he needs to move around a lot And that was really useful for avocados because there was a huge distribution of this fruit and call survive But in some point this animal disappeared and but humanity appeared and Also, we discovered that avocado were amazing Nowadays avocados are trendy food and for me I am a bit worried about the prices of avocados because trendy food sometimes people Increase the prices Well for that I analyze the prices We wanted to visualize the prices of avocados in a range of years with With bokeh bokeh is a model that allows us an interactive produced interactive plots in a really easy way Of course this script is a bit summarized. I forget to tell you that we I summarize a bit the scripts because it's too long. It's a lot of examples But all the information is available in my github that I'm gonna give you Later, don't worry if you see that it's only some short pieces of the script well Sorry, as I was telling you that it's a really simple way to do it We read the data and then we Choose the the characteristics that we want to use in our The style that we want to use in our plot in this case Dots and lines and well, we're gonna try to Trial yeah, well the the dots is um it's a distribution of the prices In the lines is the Average of the prices and the different colors the blue it's organic and the red is conventional as you can see we have a different Uh different prices, but the tendency in time it's similar well This about uh avocados My next topic or my next story is about virus because I sorry because virus are amazing Organisms But do you know that the still nowadays scientists are not sure if are alive or not? It's kind of a amazing topic, but sometimes produces A lot of illness And a lot of problems This is the case of virus zika that The information that we have nowadays is that it's transmitted by mosquito And from the family areas, we don't have vaccinations to prevent the the illness And because the symptoms we have if we are infected we can all have Fever rush and pain and the most serious and dangerous is microcephalia in newborns And here is the distribution of Of the virus nowadays And the most important thinking in When we are talking about viruses or Illness is whole fast. That's the spirit For that we can use Networks that is a model that help us to visualize The network to generate the network In this case, we are going to analyze cases of illness in brazil The first we generate a A graph or plot with different nodes that represent different cities of brazil And we are going to see who was the evolution of the spirit of this virus Let's see Well, this is the difference The different cities we have different colors that represent the the amount of Of cases as you can see it's in range in every time that Go from one range to another grow the the size of the Of the ball and also change the color I was preparing the talk. I was thinking wow, it's amazing how python can help biology, but I was a study and using a bit of machine learning and things to say yeah, but I can see also biology in python How can this How And I I start to say yeah, I think that biology inspired computing I and I want to share with you this point of view One example there are many of these examples. Well, one example is the evolutionary allegory in Specifically in this case, this is one of the examples that I love it For that I choose it, but it's ants colony optimization In this case it's based in in ants ants Can go to the nest to the to the food Because they use pheromones and they can communicate one to in to another using pheromone communication and this is really useful because When they have some troubles in the way they have a rock or something They can say one or two each other. Hey, this is the easy way to arrive It's or this is shorter way to do it This is a kind of optimization process and it's similar what Or it's the base of the of these algorithms But it's not the only one of course we have also The neural networks neural networks is based in our brain specifically in neurons Neurons communicate one or two each other with electrical inputs and Go from one to each other Imagine that we have an An input you can see something you receive information You have an input and then this information is going from one neuron to another one And then we can produce an output in this case Or whatever It's the same idea that go that is applying in artificial neural network but We need to have some things in mind that it's not exactly the same but We are gonna do an experiment. I think that it's moment to prepare yourself because I want that I'm gonna show you a picture And I need that you call How many how many seconds do you need to recognize the object in this picture? Are you ready? Yeah, okay Let's go three two one Do you need one second? Maybe raise your arm if you need one second more less less scientists It's described that our brain Needs zero point one second to recognize an object that you see before That means that if you know this object you can use zero point one second It's really fast. It's really efficient our brain What uh, what our brain or what our body is doing is analyzing this picture We are analyzing shapes. We are analyzing colors. We are analyzing by small parts similar what this doing some machine learning and here I'm gonna talk a bit about by torch model I don't I don't have a lot of information to say after the talk of yesterday I don't know if you were here, but it was kind of amazing guy explaining all about by torch But I would like to Only indicate two different Important Treat for me in this case We are going to load Dataset of flowers because we want to Uh, we want to identify flowers We are going to use a model called res net 50 that was pre-trained That this model it has a specific characteristic. It's based in pyramidal cells that mean that this These cells are not using liar by liar. The cells is go. It how can Um send information from one liar to another Far away and this is what this model also do In this case we train and also evaluate and also test And here we have the results. We have an image classification with different, um, plan species But sometimes this is amazing and works good, but needs time and money And sometimes we don't have this time This is the example. This is the case for the the next example that it's about the snakes and parter Imagine that you have a friend who is on holidays And so two different snakes take two pictures And and send to you this picture and say hey You know, I know that you know biology and also python Can you help me evolve to if I am in danger? It's fine the situation what I can do and of course This person sent to you Perfect pattern Clear, you know, like real life real data All amazing you can see all the pattern And for that we can use this model also This this model, uh, we can analyze the pixels of the images Or well, we have another option because maybe You can remember this poem that it's that say Red torch yellow kills a fellow red torch black Venom luck but maybe You have bad memory as me and you don't remember if goes kills a fellow keys a fellow Okay, no better use an script in python. It's uh, it's safe It's safety In this case, we read an image I generate a clear scales only to simplify I get A middle line of pixels and then I translate to obtain the colors And that it's what we have this is the image that your friend saw in In the nature and this is the patterns that you obtain And after that you can say, hey, you are afraid Go to the right because the left it's a venous one The biological strategy of this snake. It's uh, if this is not a venous snake It's um, it's a snake that imitate only the colors to be a safe of the predators I'm sorry Well, my last story Is who does happiness look like do you have an idea? Do you have an idea who does happiness looks like? No, no, okay. Well, first of all Uh, description of happiness overall appreciation of one's life as a whole Well, it's one definition of happiness But after that is it I want to know what is the world happiness Countries in this world Based in the world happiness report of this year. These are the top five Countries if you are from one of these Of these countries, please share with all of us What what is the secret and please Because we need to learn Why and how arrived there? Well, imagine that you want to visualize the happiness We can use this um This model that That is called rd kit And really easy way we can use the smile that it's a chemical formula We can transform these formulas and we can visualize the happiness Here we have the four or hormones in humans that are related with happiness It's that all now we have a lot of models and packages Related with biology and science only briefly Two words about ecopy ecopy it's a It's a model used in ecology and we can measure the diversity Factors My take home results are The following the forward python helped to scientist and as in this specific case in To biologists as you see but Biology is helping to computing or inspiring to computing and also to python If we work together the scientists start to collaborate more with tech people and Or if we normalize python in in science We can increase the diversity in the community and this and reach python and enrich all of us And of course if you have some idea of model package, please do it Do um do the Generate more tools because even you think that it's not uh not so important really There are a lot of people who is using these tools And oh no mostly Well, this is what happened with a biologist made python And I I finished only saying that all the information it's available in my github Uh, oh And uh, thank you very much and I hope that you enjoy the talk Thank you What what happened like what what introduced you to python Um When I was doing my phg, I realized that there was a lot of manual task that was not Has no sense to be in these years doing this task by hand or not automatically way and even I try to Che introduce some changes, you know the changes needs time and in academia Uh, it's quite conservative and When I finished and I was With my own I decided to to explore all these All all these interests that I had to Do the things more automatically and More effective way Thank you