Bioinformatics or B101nformatics

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

I am used to search in the web for the vignettes of the packages, but sometimes it is useful to access the one in the computer. In this occasions you can use: vignette(package="UpSetR") # To know if there are vignettes and their name vignette("set.metadata.plots", package = "UpSetR") # Open one of the vignettes

My research group has three bioinformaticians, but the team is mostly wet lab focused. So I consider myself and my colleagues as pet bioinformaticians . I could also be considered a clinical bioinformatician , and I want to share my (little) experience so far: Communication My lab is mostly wet lab but my boss has several bioinformaticians, despite not understanding much the mathematical/technical aspect of what we do. She is mostly interested in which genes are up-regulated, or which microorganisms are involved in the disease (inflammatory bowel disease). It is often difficult to explain my concerns with using some methods. For instance, she wants to know which microorganisms are related to which genes from the mucosal intestine. She frequently asks me for the correlations between them, without considering that this way we might have lots of noise from different sources like the diet that different patients follow. At the same time I also need to make is easy to understand the m...

For biologists using microarrays or sequencing one of the most intersting things is finding if a pathway related to a function is activated or not. To know if a pathway is activated or not usually we need to compare the same pathway in two conditions. It means a subject centered functional scoring method. Which in turns assumes that a pathway is conserved among people and time.   In addition the assumption that is done is that more expression of more genes of a pathways imply an increase of the metabolism of that pathway, which might not be true. Given that pathway has 5 genes, and that all of them are positive regulated implies that a pathway is activated? I have to dive to the origins of this, and see if there is some other way to measure how active a pathway is.

Until recently I didn't notice the changes on gene ontolology. For me it was a very reliable and stable resource. As my package BioCor is compared with GOSemSim which calculates similarities based on the gene ontologies I found that they change very much. There are constant changes on which terms are removed. I found that changes are shared via a github repository geneontology/go-announcements , which allows one to oppose to some changes.