Bioinformatics or B101nformatics

Since some time I am working with Crohn's Disease. One of the problems with the disease is that it is not known what happens. People has found associations with microorganisms, but the relationship between those microorganisms and the patient is still unknown. Also the risk factors for complications is largely unknown. This post follows up the use of a patient cohort data enrolled for identifying the risk factors of complications and health-care costs in pediatric and adult onset Crohn’s disease. Where we can see some usage of the data and the problems of unclear descriptions when using the same data. Articles describing the RISK cohort The first mention to the RISK cohort I could found is in this article [1] where they describe a cohort as: an observational research program that enrolled patients younger than age 17 diagnosed with in flammatory (nonpenetrating, nonstricturing) CD from 2008 through 2012 at 28 pediatric gastroenterology centers in North America. In that ar...

If you are developing a software you might be using a version control (If not do it :). Bioconductor until 05/2017 is using svn. However it is migrating to git, meanwhile a hybrid system is provided, where one submits the project through GitHub using git control version system and internally it uses svn. Here are some experiences developing in for Bioconductor in this configuration . After following the recommendations of the configuration .git/config ends up with: [core]     repositoryformatversion = 0     filemode = true     bare = false     logallrefupdates = true [remote "origin"]     url = https://github.com/llrs/BioCor.git     fetch = +refs/heads/*:refs/remotes/origin/* [branch "master"]     remote = origin     merge = refs/heads/master [remote "bioc"]     url = https://github.com/Bioconductor-mirror/BioCor.git     ...

Gene Set Enrichment Analysis is a test thought to find if the position of a group along a list implies some difference. The most know method is the one maintained by the Broad Institute . As it was the first widely used in biology and holds several collection of gene sets. A gene set is a collection of genes related, by either a function or an experiment, it is as fuzzy described as a pathway. In Bioconductor there is the under used tool of BiocViews , a topic for package classificacion. We can find a category for GSEAs under Software>BiologicalQuestion>GeneSetEnrichment . This category list 74 packages at the time of writing, which provide function for Gene Set Enrichment Analysis. It will be too long (and too hard for me) to describe all the packages in that category. However, it doesn't include all the packages that perform gene set enrichment. The first package for GSEA in Bioconductor one should look is GSEABase which provides with tools for reading files from...

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...

After some trouble I must say that in public: If you have a big task which takes many time and decide to parallelize. DO NOT PARALLELIZE EVERYHING! Otherwise you will have a parallel task inside another parallel task! Just a friendly reminder :D