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Big Data: Is not only a fancy/catchy name
The field of biomedical research has a new trend to use fancy terms in the title of papers/grants in order to attract the attention of reviewers, journals and grant agencies. Amount others are:...
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Data Visualization: Plots You Should be Using More
Inspired by this blog post1- Parallel Coordinates— A parallel coordinates graph arrays multiple variables alongside one another with each scaled from highest to the lowest value (highest at the top,...
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Monit: Monitoring your Services
Bioinformatics Applications are moving more in the direction of "Microservices" Architectures where services should be fine-grained and the protocols should be lightweight. Microservices Architectures...
View ArticleCode Cost: Write less code
Based on @UmerMansoor Not too long ago, I sat down to ‘clean up’ a project that I inherited. I was given the reins of the refactoring efforts because the project has had several bugs in production. It...
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BioDocker Announcement
The BioDocker web page is out: biodocker.orgThe Documentation: biodocker.org/docsThe GitHub: github.com/BioDocker/Registry: hub.docker.com/u/biodckr/
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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...
View ArticleUseful Links to prepare your presentation or talk
Creating effective slides: Design, Construction, and Use in Science:
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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 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...
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...
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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-...
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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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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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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...
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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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 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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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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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...
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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