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EMBnet.digest August 2016
A Quick Guide to IMGT/Junction Analysis

Bioinformatics

Applied Bioinformatics Course

An online teaching resource for applied bioinformatics.

Chipster - open source platform for data analysis

Chipster is a user-friendly software for analyzing high-throughput data such as NGS and microarrays. It contains over 350 analysis tools and a large collection of reference genomes. Users can save and share automatic analysis workflows, and visualize data interactively using for example the built-in genome browser. Chipster's client software uses Java Web Start to install itself automatically, and it connects to computing servers for the actual analysis. Chipster is open source, and the server environment is available as a virtual machine image free of charge.

MRS: A fast and compact retrieval system for biological data.

The biological data explosion of the 'omics' era requires fast access to many data types in rapidly growing data banks. The MRS software provides the tools to rapidly and reliably download, store, index, and query flat-file databanks. Data stored and indexed by MRS takes considerably less space on disk than the raw data, despite that these raw data are included. The MRS index information is part of the stored data. Therefore, public and private data can be combined by simple concatenation and thus without computational overheads....

wEMBOSS

wEMBOSS is a web interface to the popular EMBOSS software package for biological sequence analysis. wEMBOSS is a coordinated effort from Martin Sarachu of the Argentinian EMBnet Node and Marc Colet from the Belgian EMBnet node...

EMBOSS

EMBOSS is "The European Molecular Biology Open Software Suite". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit.

eBiotools

Many MacOSX packages and software for Bioinformatics.

EMBnet.journal

EMBnet.journal is an international, Open Access, peer-reviewed journal whose primary goal is to provide biomedical scientists with practical information to help 
  • Tackle routine data-analysis tasks (whether basic or advanced)
  • Implement complex, multi-faceted IT architectural infrastructures
  • Address the many new challenges of modern, data-driven Life Science research.

RegulonDB

RegulonDB (http://regulondb.ccg.unam.mx/) is the primary reference database of the best-known regulatory network of any free-living organism, that of Escherichia coli K-12. It has expanded its biological context so that transcriptional regulation is now part of a unit that initiates with the signal and continues with the signal transduction to the core of regulation, modifying expression of the affected target genes responsible for the response.

Next Generation Sequencing Data Analysis Network - SeqAhead

Next generation sequencing (NGS) is a highly parallelised approach for quickly and economically sequencing new genomes, re-sequencing large numbers of known genomes, or for rapidly investigating transcriptomes under different conditions. Producing data on an unprecedented scale, these techniques are now driving the generation of knowledge (especially in biomedicine and molecular life sciences) to new dimensions. The massive data volumes being generated by these new technologies require new data handling and storage methods.

Broadening the Bioinformatics Infrastructure to unicellular, animal, and plant science - AllBio

The completion of the human genome sequence has triggered worldwide bioinformatics efforts to unravel its information content. Many projects have been successfully completed in areas such as gene hunting, functional annotation, post-translational modification prediction, protein-protein interactions, transcriptomics, or systems biology. These projects have produced large numbers of novel analytic and predictive computer programs.

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