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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
http://sourceforge.net/projects/laitor/
A text mining software developed to find co-occurrence of biological entities (gene/protein terms) together with biointeractions and concepts term from customized dictionaries.
Proper citation: LAITOR (RRID:SCR_012101) Copy
http://matnmr.sourceforge.net/
A highly flexible software toolbox for processing 1D and 2D NMR and EPR spectra under MATLAB, creating high-quality 1D, 2D or 3D plots from the spectra and printing them in every type of format that is supported by MATLAB.
Proper citation: MatNMR (RRID:SCR_012060) Copy
http://www.computationalbioenergy.org/meta-storms.html
Optimized GPU-based software to efficiently measure the quantitative phylogenetic similarity among massive amount of microbial community samples.
Proper citation: GPU-Meta-Storms (RRID:SCR_012029) Copy
http://www1.montpellier.inra.fr/CBGP/diyabc/
Software to make Approximate Bayesian Computation inferences about population history using Single Nucleotide Polymorphism, DNA sequence and microsatellite data.
Proper citation: DIYABC (RRID:SCR_012031) Copy
https://code.google.com/p/metextract/
A software tool for scientists working with stable isotopic labelling and high resolution liquid chromatography mass spectrometry.
Proper citation: MetExtract (RRID:SCR_012048) Copy
http://mzmine.sourceforge.net/
Software for mass-spectrometry data processing, with the main focus on LC-MS data.
Proper citation: MZmine (RRID:SCR_012040) Copy
Community building portal that serves over 3,000 members from more than 70 countries by addressing scientific policies, providing access to high quality publications, organizing meetings, and serving as a portal to information about training, education, employment, etc.
Proper citation: International Society for Computational Biology (RRID:SCR_012009) Copy
http://sourceforge.net/projects/exorca/
A Matlab package extending the scope of established COBRA metabolic modelling.
Proper citation: ORCA (RRID:SCR_012097) Copy
http://opencobra.sourceforge.net/openCOBRA/Welcome.html
Software Python package that provides support for basic COnstraint-Based Reconstruction and Analysis (COBRA) methods.
Proper citation: COBRApy (RRID:SCR_012096) Copy
http://knowtator.sourceforge.net/
A general-purpose text annotation tool that is integrated with the Prot����g���� knowledge representation system.
Proper citation: Knowtator (RRID:SCR_012099) Copy
http://sourceforge.net/projects/pb-jelly/
Software that automates the finishing process using long sequence reads in a reference-guided assembly process.
Proper citation: PBJelly (RRID:SCR_012091) Copy
https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/AHA
Contigs from a draft assembly generated by a different assembler can be joined using PacBio long reads.
Proper citation: AHA (RRID:SCR_012090) Copy
https://code.google.com/p/netcoffee/
A fast and accurate algorithm which allows to find a global alignment of multiple protein-protein interaction networks.
Proper citation: NetCoffee (RRID:SCR_012095) Copy
https://code.google.com/p/qsimscan/
A flexible open source protein similarity search software tool which provides a significant gain in speed compared to BLASTP at the price of controlled sensitivity loss.
Proper citation: PSimScan (RRID:SCR_012094) Copy
http://www.few.vu.nl/~mavdwiel/ShrinkBayes.html
Software for detecting differential features across the entire spectrum, including the lower counts.
Proper citation: ShrinkSeq (RRID:SCR_012022) Copy
A genome browser specialized in next-generation sequencing data.
Proper citation: GenomeJack (RRID:SCR_012026) Copy
Specializes in sequence and array-based SNP and copy number analysis, genetic association software, and analytic services. Their technologies empower scientists to determine the genetic causes of disease, transform drug discovery, develop genetic diagnostics, and advance the quest for personalized medicine.
Proper citation: Golden Helix Incorporated (RRID:SCR_012191) Copy
https://code.google.com/p/glycanbuilder/
An intuitive and flexible software tool for building and displaying glycan structures.
Proper citation: GlycanBuilder (RRID:SCR_012123) Copy
https://code.google.com/p/glycresoft/
A software package for automated recognition of glycans from LC/MS data.
Proper citation: GlycReSoft (RRID:SCR_012122) Copy
Proper citation: Ministry of Health and Family Welfare - Government of India (RRID:SCR_012124) Copy
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