Bioinformatics or B101nformatics

My experience with Bioconductor I been involved with the Bioconductor project for several years and last year I attended the BioC2019 conference in New York. It was my first time in an international conference abroad. I'm posting here my experience with the project. Pre-conference The first time I heard about Bioconductor was in 2013 when in an internship, my main goal was to analyze data from Pichia pastoris and look at the functions of the differentially expressed genes through gene ontology. I did it with topGO and other packages included in Bioconductor. Later during the master in Bioinformatics for Health Science I studied, we used several packages from Bioconductor to analyze other data (the main project is still online ). Also as part of the master thesis I also used some other packages (the thesis involved using WGCNA ) but the main question roadblock was knowing the function and what are the genes doing. So I developed a package to compare the annotation of genes accord...

If you have a package in Bioconductor and you need to change the email (say you change from university or company) it is not fast. You need to do the following: On the bioc-devel mailing list. On the support website through "edit my profile" On your BiocCredentials Send a request to the bioc-devel for updating the maintainer email for the related packages  Update the DESCRIPTION file in the release and devel branches of all the packages the email is listed in (this can be done by Bioconductor core members if you ask so in the previous point) This is because there isn't a centralized account to control the email on all these related services. It is not hard, but you could forget something. Thanks to Leonardo and Nitesh for reporting this on the mailing list

One of my last post was " I don't do machine learning ". Now, I realized that I am actually doing it (more on this below). However what I was doing previously? I would say I was doing data learning . What is different in machine learning to methods? After reading a lot, I think that the differences are on the focus, a regression (substitute for other procedures that model something) can be used for both machine learning and data learning. When I do a linear regression in data learning I focus on which variables have more weight and improve the adjusted R 2 . I learn from the data what is happening . When I do machine learning I focus on which linear regression is better with the data I have (or with new data). I learn from the data what models are better. That model can be a simple regression or a complicated deep neural network. Both have the same data, but the goal is different. Of course, nowadays where it is not too computationally expensive we want both: ...

Yesterday I received an amazing email: Congratulations, BioCor has been added to Bioconductor! Yes, I had submitted a package for the Bioconductor project at the beginning of the week. The package calculates similarities between pathways, genes and clusters of genes based on their pathways. A pathway is a group of functionally related proteins, thus this similarities calculates the functional similarity of the pathway or genes in question. If anyone is curious what the email had this was in the body (I didn't know what to expect when I knew that it would be accepted):  Hi Lluís, Congratulations, BioCor has been added to Bioconductor! Currently, the definitive location for your Bioconductor package is in our SVN repository. The following information is to help you in your role as a package maintainer. You’ll need the following credentials to maintain your package: Subversion user ID: myuser Password: mypassword Package ‘landing pages’ Every package in Bi...

Recently Google came up with Google Genomics  to store genomes and work with them. The easiest way to explore it is through their genome browser ( GA browser ).  Position 132564975 of chromosome 7 of genome HG01440 from the Google repository of the 1000 Genomes Project. Which are the next steps? For developers it has come up with a new API . The system is currently in open beta , so the income of comments and early adopters is going on. This is part of the feed back I want o give as well as some thoughts about it. Improve help pages In my experience a better documentation is better than a better version. What do I mean? I try to do more with less time, when I look for help I want a quick and easy (to follow) answer (if possible). Thats why Stack Overflow  has so many questions, or why the mailing list are open, to help more people with less effort. In fact the help is now divided between Stack Overflow' tag g oogle-genomics  and google-genomics-api...

Probably  you have heard about blast. It helps to find homologous sequences, it can be use through different variants with proteins, genes or just partial sequences to try to find what it is. It can be used also for proteins but there is another tool which can compete with it: HMMER In this article I will describe how I used it to find which kind of protein do we have. HMMER, like blast, has a family of functionalities but it was originally thought as a tool to find homologous proteins through a Hidden Markov Model . At the date of publication has four main functionalities ( hmmsearch jackhmmer hmmscan phmmer ) that can be used online. I will center in hmmsearch, the main tool, which we can run locally after downloading the software, I assume in this post that you are working with a computer with some of the Linux distributions and that you already downloaded the HMMER software and installed it. (See the manual ) Setps We need a profile o...