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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...
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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...
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Some of the most cited manuscripts in Proteomics and Computational Proteomics...
Some of the most cited manuscripts in 2013 in the field of Proteomics and Computational Proteomics (no order): The Proteomics Identifications (PRIDE) database and associated tools: status in 2013:...
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What is a bioinformatician
By Anthony Fejes originally posted in blog.fejes.caI’ve been participating in an interesting conversation on linkedin, which has re-opened the age old question of what is a bioinformatician, which was...
View ArticleSolving Invalid signature in JNLP
I have this error each time i run my jnlp:invalid SHA1 signature file digest forI found some discussions about possible...
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In the ERA of science communication, Why you need Twitter, Professional Blog...
Where is the information? Where are the scientifically relevant results? Where are the good ideas? Are these things (only) in journals? I usually prefer to write about bioinformatics and how we should...
View ArticleMost read from the Journal of Proteome Research for 2013.
1- Protein Digestion: An Overview of the Available Techniques and Recent Developments Linda Switzar, Martin Giera, Wilfried M. A. Niessen DOI: 10.1021/pr301201x 2- Andromeda: A Peptide Search...
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SWATH-MS and next-generation targeted proteomics
For proteomics, two main LC-MS/MS strategies have been used thus far. They have in common that the sample proteins are converted by proteolysis into peptides, which are then separated by (capillary)...
View ArticleJava Optimization Tips (Memory, CPU Time and Code)
There are several common optimization techniques that apply regardless of the language being used. Some of these techniques, such as global register allocation, are sophisticated strategies to allocate...
View ArticleThesis: Development of computational methods for analysing proteomic data for...
Thesis by Markus Brosch in 2009 about Computational proteomics methods for analysing proteomic data for genome annotation.Notes from AbstractProteomic mass spectrometry is a method that enables...
View ArticlePepFinder™ Software: New Software Streamlines Protein Identification and...
PepFinder™ Software For biotherapeutic proteins to be effective, they must be produced in biologically active forms with proper folding and post-translation modifications (PTMs). Thermo Scientific™...
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ProteoStats: Computing false discovery rates in proteomics
By Amit K. Yadav (@theoneamit) & Yasset Perez-Riverol (@ypriverol):Perl is a legacy language thought to be abstruse by many modern programmers. I’m passionate with the idea of not letting die a...
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Making Your Code Citable
Original post from GitHub Guides:Digital Object Identifiers (DOI) are the backbone of the academic reference and metrics system. If you’re a researcher writing software, this guide will show you how to...
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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...
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Git useful commands
In bioinformatics GitHub and its protocol git is getting more and more popular. Here you will find an introduction about git and also some useful commands when you use Git in your projects. What is...
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What is Markdown?
Markdown is a plain text format for writing structured documents, based on conventions used for indicating formatting in email and usenet posts. It was developed in 2004 by John Gruber, who wrote the...
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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...
View ArticleNEW NIST 2014 mass spectral library
Originally posted in NIST 2014.Identify your mass spectra with the new NIST 14 Mass Spectral Library and Search Software.NIST 14 - The successor to NIST 11 (2011) - Is a collection of:Electron...
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Start a startup or Work for someone else?
Originally posted on P4P:When you look online for advice about entrepreneurship, you will see a lot of "just do it": The best way to get experience... is to start a startup. So, paradoxically, if...
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Evaluation of Proteomic Search Engines for PTMs Identification
The peptide-centric MS strategy is called bottom-up, in which proteins are extracted from cells, digested into peptides with proteases, and analyzed by liquid chromatography tandem mass spectrometry...
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