Quick Guide to the New Uniprot Web

Probably Uniprot is one of the most used and well-established services in bioinformatics worldwide. With more than 12 years, is one of the major resources of biological information and the reference catalog of protein sequence in the World. The aim of Uniprot is provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information. It started in 2002 when the Swiss‐Prot, TrEMBL and PIR protein database activities have united to form the Universal Protein Knowledgebase (UniProt) consortium.

Adding CITATION to your R package

Original post from Robin's Blog:

Software is very important in science – but good software takes time and effort that could be used to do other work instead. I believe that it is important to do this work – but to make it worthwhile, people need to get credit for their work, and in academia that means citations. However, it is often very difficult to find out how to cite a piece of software – sometimes it is hidden away somewhere in the manual or on the web-page, but often it requires sending an email to the author asking them how they want it cited. The effort that this requires means that many people don’t bother to cite the software they use, and thus the authors don’t get the credit that they need. We need to change this, so that software – which underlies a huge amount of important scientific work – gets the recognition it deserves.

What is a bioinformatician

By Anthony Fejes originally posted in blog.fejes.ca

I’ve been participating in an interesting conversation on linkedin, which has re-opened the age old question of what is a bioinformatician, which was inspired by a conversation on twitter, that was later blogged.  Hopefully I’ve gotten that chain down correctly.

In any case, it appears that there are two competing schools of thought.  One is that bioinformatician is a distinct entity, and the other is that it’s a vague term that embraces anyone and anything that has to do with either biology or computer science.  Frankly, I feel the second definition is a waste of a perfectly good word, despite being a commonly accepted method.

Are you a Computational Biologist or Bioinformaticist or Bioinformatician?

A recent discussion was provoked by @attilacsordas on twitter January 8 regarding what is the choice term for referring to those researchers working on Bioinformatics and Computational Biology fields.

Are bioinformaticians and bioinformatists alike? :)
— attilacsordas (@attilacsordas) January 8, 2014

This debate is older than people may think and it looks like an insignificant topic, but when you are writing your CV or your internet profile, or you’re looking for a new job, you will need a professional title, and that is really important. If you also look the volume of discussion and opinions about this topic on internet you will realize that the community have different points of view. I've use some of my spare time to read in detail different opinions about it, and also collect some those opinions and articles. Let’s see what common terms are used nowadays for these researchers:

Bioinformaticist, Bioinformatician, Computational Biologist, Digital biologist, bioinformatics analyst

My Formula as a Bioinformatician

Every day, I enjoy reading about bioinformatics in blogs, linkedin, and twitter; away from my daily reading of manuscripts journals. I strongly think that the future of publications/science will be closer & closer to the open access style and this emergent way to publish your ideas faster/brief in your own space. Some of my old co-workers don't understand this way to get in touch with science using informal environments rather than arbitrary/supervised spaces; I just said to them, we make the future, not the past. Reading the popular post “A guide for the lonely bioinformatician”, I was thinking about the last three years and how I have been built my own formula to survive as a lonely bioinformatician in a small country, with a lousy internet connection and without a bioinformatics environment.        

All the bioinformaticians that I met during these three years can be categorized in three major groups considering their original background:

1)    MDs, Biologist, Biochemist, Chemist
2)    Physicist, Mathematicians, Computer Scientist, Software Engineers, Software
       Developers
3)    Philosophers, *

As an embryonic and growing field the diversity is huge, then it is quite complex to express all the data behavior in one model or a formula. Here I will summarize some of the variables of my formula, extremely correlated with the original post suggestions: