“When a biologist met Python”

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“When a biologist met Python”
An adventure into the natural sciences using tools like Biopython, Bokeh, Networkx, Ecopy and more!
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Biology and computing are closer than we usually think, for example many algorithms are inspired in biology patterns, and complementary to that, researchers needs special algorithms to have a better understanding of our environment. Thus, there is a strong relation an dependency. In the past years, Biology has been transformed into computational biology. Therefore technological advances helps us to predict physical interactions between atoms and DNA, because we are being able to integrate information from biology into algorithms. Python has become a popular programming language in biosciences because it has a clean syntax that makes it easy to read language. In addition to this, there are many modules (toolkits) extending to different biological domains, like metabolomics, structure analysis, phylogenomics, molecular biology and others. Python is currently improving researcher’s workflow, helping us to focus on the theory or experimental part, instead of fighting with old buggy applications. This talk aims to be oriented to all audiences (with/without biological background) since we will go together through an amazing adventure into the natural sciences using tools like Biopython, Bokeh, Networkx, Ecopy and much more! Are you brave enough to follow me on this journey?
Keywords Algorithms Data Science Natural Science Scientific Libraries (Numpy/Pandas/SciKit/...) python
Inclusion map Googol Multiplication sign Point cloud Annulus (mathematics)
Point (geometry) Metre Parsing Multiplication sign Adventure game Open set Mereology Graph coloring Field (computer science) Product (business) Mathematics Different (Kate Ryan album) Term (mathematics) Number theory Oval Endliche Modelltheorie Sensitivity analysis Computing platform Adventure game Scripting language Distribution (mathematics) Computer virus Electric generator Information Moment (mathematics) Shared memory Planning Database Product (business) Distance Data management Uniform resource locator Wave Personal digital assistant Video game Energy level Spacetime
Scripting language Dot product Distribution (mathematics) Information Clique-width Plotter Range (statistics) Characteristic polynomial Bit Line (geometry) Average Graph coloring Plot (narrative) Circle Average Self-organization Endliche Modelltheorie Alpha (investment)
Computer virus Computer virus Graph (mathematics) Information Multiplication sign Plotter Range (statistics) Thermal expansion Graph coloring Heegaard splitting Software Different (Kate Ryan album) Personal digital assistant Personal digital assistant Devolution (biology) Endliche Modelltheorie Family
View (database) Multiplication sign Set (mathematics) Function (mathematics) Shape (magazine) Mereology Dressing (medical) Neuroinformatik Medical imaging Different (Kate Ryan album) Active contour model Endliche Modelltheorie Algorithm Sampling (statistics) Bit Process (computing) Telecommunication Allegory output Pattern language Species Functional (mathematics) Resultant Impulse response Point (geometry) Twin prime Ant colony optimization algorithms Real number Virtual machine Similarity (geometry) 2 (number) Software testing output Mathematical optimization Modem Ant colony optimization algorithms Information Artificial neural network Direction (geometry) Weight Cellular automaton Plastikkarte Computer network Genetic programming Personal digital assistant Function (mathematics) Video game Object (grammar) Mathematical optimization
Pixel Divisor Multiplication sign 1 (number) Online help Graph coloring Medical imaging Mathematics Strategy game Natural number Computer configuration Semiconductor memory Well-formed formula Active contour model Software testing Endliche Modelltheorie Message passing Traffic reporting Descriptive statistics Software development kit Task (computing) Scripting language Scaling (geometry) Information Open source Shared memory Line (geometry) Virtual machine Word Message passing Personal digital assistant Video game Right angle Pattern language Musical ensemble Active contour model
thank you very much for coming um first thing that I would like to do is sharing my feelings because this is my first tech conference and I am really scared 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 in molecular biology and after a while I was a science if stay in academia or go to industry and in this time I start to learn Python because I knew that it was useful for science and it was kind of I mean in this point I discover 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 ow this is amazing why I didn't start to use it before this moment well I decided to move to industry we're in working as a product manager ecommerce platform that we sell products or scientist and one of my role was looking for numerous new resources in this case publication and it was in that moment when I realized and I discover some amazing tools but I thought why I cannot share with the wall this new discovery and that it's why I am here today well this this talk is not a conventional talk we're gonna have biological adventure but with Python that means that we are going to cover some different biological topics and how Python can have a role in this as you can see will really different topics my first story it's about plants because plants are amazing they are there and they cannot work they can not speak but even that they can communicate one of eight dollars imagine the situation we are in
our living room we have a plan but it's living there really happy and this plan are safe or see the light with two different kind of waves but we thought it's amazing situation but maybe I can buy a new plan I'm there because my plan is really happy there I can't have a know anyone near and in this situation you are right to your home and this second plan also see the life - the same way but this plan also reflect a kind of wave saying that one plan can detect to another and they are started to be unhappy because they aren't feeling that they are in dangers they need to survive because they are in competition for light amazing topic if this was my topic of this is and imagine that you want to know about this syndrome but it's the generative for this situation that is complete the void and seed room and this is where Python can help us we can use this model called via 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 land side and also I am looking for terms I choose this this database because contain open access publications but there are many others databases that you can look a lot of kind of information to like with different fields on in 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 cannot change we solve for text and other information and we can see that this also has two different publications in open access at journals sorry well I'm sorry I mean I give you an exposure for the magnet the story but I wanted to say the last thing remember if you have to plant really close at home give Lee give some space to them they will be happier may make the story it's a love avocado because I woke up oh it is from other era I don't know if you know that but this is the aspect that the primitive avocado was hot the the seed was huge and this was a really problematic issues because they it's really difficult the dispersion of this of this seed but thanks to this dynamo well not these to thank dumb grandparent but they would I yeah and a lot around 4 meters of rice that ate our colors we have avocados nowadays but you can think yeah but this is an animal around 4 meters only about color 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 about colors because there was a huge distribution of this fruit and go survive but in some point these animal disappear and but humanity appear and so we discovered that avocado were amazing nowadays avocados are a trendy food 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 I
wanted to visualize the prices of avocados in a range of years with bacca bacca the model that allows us an interactive produced interactive plots in a really easy way of course this 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 wanna give you later don't worry if you see that it's only some sure pieces of the scape well sorry as I was tell you it's a really simple way to do it will read the data and then we choose the characteristics that we want to use in our the style that we want to use in our dots and lines and well we're gonna try to try oh yeah well the dotted
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 different prices but the tendency in time it's similar well this about avocados my next topic on our next story it's about virus because I'm sorry because viruses are amazing organized but do you know that still nowadays scientists are not sure if are alive or not it's kind of amazing topic but sometimes produce a lot of illness and a lot of problems this is a car the case of by Rosica that the information that we have nowadays it that it's transmitted by mosquito and from the family is we don't have vaccination to prevent the illness and because the symptoms we have if we are infected we can have fever rash and pain and the most serious and dangerous is microcephaly in newborns here it's the distribution of of the buyers nowadays and the most important think in when we are talking about viruses or illness is how fast does it was played for that we can use network but it's a model that help us to visualize the network to generate a network in this case we are going analyzed cases of illness in Brazil the first we generate a graph or plot with different nodes that represent different cities of Brazil and we are gonna see how was devolution of the split of this virus let's see now well this is the different 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 wandering to
another grow the size of the of the ball and also change the color when I was preparing the talk I'm thinking wow it's amazing how Python can help biology but I can't see also biology in Python who can this oh yeah I think that biology
inspired computing and I want to share with you this point of view one example there are many of this example well one example is the Volusia nary allegory in specifically in this case this is one of that samples that I love it for that I chose it but it's ant colony optimization in this case its base in ignant ants can go to the nest to the to the food because they use pheromones and they can communicate one twin to another using pheromone communication and this is really useful because when they have some travels in the way they rock or something they can't say one or two each other hey this is the easy way to arrive it or this is shorter way to do it this is a kind of optimization process and it's similar at what good 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 net worth is based in our brain specifically in neurons neurons communicate one or two each other with electrical impulse and go from one to each other imagine that we have an input you can't see something you'll receive information you have a 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 ago that it's 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 momen to prepare yourself because I want that I'm gonna show you a picture and I need the Duke card 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 a dress you harm if you need one second more less less scientist it's the scribe that our brain needs 0.1 second to recognize an object that you see it before that means that if you know this object you can use 0.1 seconds it's really fast it's really efficient our brain what what our brain whatever what is doing is analyzing this picture we are analyzing shapes when analyzing who analyzing by a small part similar what is doing some machine learning I'm here I'm gonna talk a bit about PI third 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 ok explaining all about pie tart but I would like to only indicate two different important treat for me in this case a lot data set of flowers because we want to do we want to identify flowers we are going to use a model called resonate 50 that was pre-trained it that this modem it has a specific characteristic its base in pyramidal cells that mean that this the cells are not using layer by layer the cells is ago it can send information from one layer 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 image classification with different plant species at some time this is amazing and was good but needs time and money and sometimes we don't have this time this is that sample this is the case for the next example but it's about this nation pattern imagine that you have a friend who is on holidays and so two differences name take two pictures and and send to you this picture say hey you know I know that you know biology and also Python can you help me evolve too if I am in danger it's fine the situation what I can do and of course this person sent to you a perfect pattern in clear you know like real life real data amazing you can see on the pattern and for that we can
use this model also this this model we can analyze the pixels of the images oh well we have another option because maybe you can't remember this poem that it's that's a red tote yellow kills the fellow red tote black Benham luck but maybe you have bad memory as me and you don't remember it goes kills the fellow kiss the fellow kill okay no better use a script in Python it is safe safety in this case we're it an image I generate three scales only to simplify I get middle line of pixels and then I translate to obtain the colors and that it what we have this is the image that your friend so in nature and this is the pattern that you obtain and after that you can say hey you are a face go to the right because the left it's a very nice one the biological strategy of this snake its if this is not a banana snake it its neighbor imitate Oh the colors to be a safe of the Deaf predators I'm sorry well my last story is told us happiness look like do you have an idiom do you have an idea who does happiness looks like now no okay well first of all description happiness overall appreciation of one's life as a whole well it's one definition of happiness but after that you see I want to know what is the world happiness countries in this world basing that world happiness report of this year is at the top five countries if you are from one of these of these countries please share with all of us what is the sacred and please because we need to learn why and home arrived there well imagine that you want to visualize the happiness we can use this this model that is called RT 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 for our hormones in humans that are related with happiness it's at all now we have a lot of models and packages related with biology and science only briefly to words about occupy occupy it it's a model used in ecology and we can measure the diversity the factors my take-home message are before we for one - help - scientist innocent in this specific case in by l2 biologists as you see but biology is helping to computing or inspiring to computing and also to Python if we work together these scientists start to collaborate more with tech people and if we normalize Python in in science we can increase the diversity in the community and this enriched Python and enriched all of us and of course if you have some idea of model package please do it call our - to generate more tools because even you think that it's not not so important really there are a lot of people who is using these tools and no no Muslim well this is what happened with a biologist made Python and I finished only saying that all the information it's available in my github oh and thank you very much and I hope that you enjoy the talk thank you [Applause]
when I was doing my apt I realized that there was a lot of manual tasks that was not has no sense to be in these years doing this test by heart or not automatically way and even I try to change introduced some changes you know the changes needs time and in academia is quite conservative and when I finish and I was with my own I decide to explore all these all these interests that I had to do the things more automatically and more effective way [Music] [Applause]