NEW 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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I love technical notes and short manuscripts
One of my first papers in 2012 (here), was related with support vector (SVM) machines. It was a simple algorithm, that improved the method to compute the isoelectric point of peptides using SVM. The...
View Articlefirst tweet with more than 1k rt and my post with more than 5k
Happy to see my first post with more than 5k visits: Introduction to Feature selection for bioinformaticians using R, correlation matrix filters, PCA & backward selectionand my first tweet with...
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one big lesson I just learn
I'm coming from small country with no resources, no big industries or capitals (Cuba); but with a big tradition in friendship and solidarity. In my previous institute (surprisingly, a big biotech...
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The future of Proteomics: The Consensus
After the Big Nature papers about the Human Proteome [1][2] the proteomics community has been divided by the same well-known topics than genomics had before: same reasons, same discussions [3-7]. No...
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...
View ArticleProteomics & personalized medicine Issue in Proteomics
A new issue in Proteomics was recently edited and published by René P. Zahedi et al. regarding proteomics and personalized medicine. This Focus Issue comprises a total of eight valuable contributions...
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Moving Bioinformatics to the Cloud
Constantly we presence new technologies being developed and streamed to public, to researchers that work with molecular biology, the ones that get our attention normally comes from new laboratory...
View ArticleDIA-Umpire Pipeline Using BioDocker containers.
By +Felipe Leprevost and +Yasset Perez-RiverolThe complexity of some bioinformatic softwares is well-known and it has been commented in different papers and blog posts, etc. Especially, those...
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An API for all MS-based File formats
We recently released and published our first Java API (Application Programming Interface) for the most common file formats in proteomics, not only ms files but also identification files such as...
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First Scrum Board
Here, my first Scrum board to guide the release of OmicsDI project.Team members update the task board continuously each sprint; if someone thinks of a new task (“test a new machine learning...
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The end of the big files nightmare in Github
One of the nightmares of Github was always the Big Files. The previous limit in 100MB made difficult to test applications with real examples demanding a lot of work to create "dummy" test files. Today...
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Installing MESOS in your Mac
1- Homebrew is an open source package management system for the Mac that simplifies installation of packages from source.ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)"2-...
View ArticleProtein identification with Comet, PeptideProphet and ProteinProphet using...
By +Yasset Perez-Riverol and +Felipe Leprevost:Proteomics data analysis is dominated by database-based search engines strategies. Perhaps the most common protocol today is to retrieve raw data from a...
View ArticleGenome Mapping and SNP Calling with BioDocker
#http://www.htslib.org/workflow/#mapping_to_variantset -xeuFQ1=y1.fastqFQ2=y2.fastqREF=yeast.fastaBNM=yeastDRUNINDOCKER=1SAMTOOLS=samtoolsBWA=bwaTABIX=tabixBCFTOOLS=bcftoolsPLOTVCFSTATS=plot-vcfstatsif...
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GitHub in Numbers for Bioinformaticians
Impact of Github in Numbers: Total Number of Bioinformatics repositories in Github: Figure 2: Number of Bioinformatics Repositories created by Years (source Github).Total Number of Bioinformatics...
View ArticleUseful Links to prepare your presentation or talk
Creating effective slides: Design, Construction, and Use in Science:
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How to estimate and compute the isoelectric point of peptides and proteins?
By +Yasset Perez-Riverol and +Enrique Audain :Isoelectric point (pI) can be defined as the point of singularity in a titration curve, corresponding to the solution pH value at which the net overall...
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