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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://fgcz-bfabric.uzh.ch/bfabric/
An open infrastructure for managing projects and data in life sciences that allows to store and access experimental data together with its scientific context. The platform connects the data from scientific instruments with data analysis tools, including workflow, annotation, and data visualization support. All public data can be searched and used to carry out inter-experiment analyses. For a fee, B-Fabric Order allows you to order the following analytical services at the FGCZ independent of a User Lab research project: Mass spectrometry, Protein sequencing, peptide sequencing, Amino acid analysis, Chromatography, Electrophoresis.
Proper citation: B-Fabric (RRID:SCR_011827) Copy
http://tron-mainz.de/tron-facilities/computational-medicine/galaxy-lims/
A laboratory information management system (LIMS) for a next-generation sequencing (NGS) laboratory within the existing Galaxy platform.
Proper citation: Galaxy LIMS (RRID:SCR_011829) Copy
http://archimedes.cheme.cmu.edu/?q=gpublast
Software for an accelerated version of the popular NCBI-BLAST using a general-purpose graphics processing unit (GPU). It s nearly four times faster, while producing identical results. GPU-BLAST supports: protein alignment according to blastp (it does not support psiblast), multiple CPU threads working in parallel with a single GPU, and input files with multiple protein queries.
Proper citation: GPU-BLAST (RRID:SCR_011820) Copy
http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastx&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
A web-based tool used to search translated nucleotide databases using a translated nucleotide query.
Proper citation: TBLASTX (RRID:SCR_011823) Copy
An easy-to-use, highly customizable genome browser you can use to visualize and explore genomic data and annotations, including RNA-Seq, ChIP-Seq, tiling array data, and more.
Proper citation: IGB (RRID:SCR_011792) Copy
http://www.broadinstitute.org/igv/
A high-performance visualization tool for interactive exploration of large, integrated genomic datasets.
Proper citation: Integrative Genomics Viewer (RRID:SCR_011793) Copy
http://www.ncbi.nlm.nih.gov/tools/gbench/
An integrated application for viewing and analyzing sequence data.
Proper citation: NCBI Genome Workbench (RRID:SCR_011794) Copy
https://code.google.com/p/ngsplot/
A software program that allows you to easily visualize your next-generation sequencing (NGS) samples at functional genomic regions.
Proper citation: ngs.plot (RRID:SCR_011795) Copy
http://www.cs.utah.edu/~miriah/mizbee/Overview.html
A multiscale synteny browser for exploring conservation relationships in comparative genomics data.
Proper citation: MizBee (RRID:SCR_011804) Copy
http://pipmaker.bx.psu.edu/pipmaker/
PipMaker computes alignments of similar regions in two DNA sequences. Moreover, MultiPipMaker can be requested to compute a true multiple alignment of the input sequences and return a nucleotide-level view of the results.
Proper citation: PipMaker and MultiPipMaker (RRID:SCR_011806) Copy
A generic sequence comparison tool for visualizing genome alignments both within and between species.
Proper citation: SynBrowse (RRID:SCR_011807) Copy
http://i122server.vu-wien.ac.at/CANGS1.1/
A user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies.
Proper citation: CANGS (RRID:SCR_011837) Copy
http://code.google.com/p/condetri/
Software tool as content dependent read trimmer for Illumina data. Content dependent read trimming software for Illumina/Solexa sequencing data.
Proper citation: ConDeTri (RRID:SCR_011838) Copy
http://www.cbcb.umd.edu/software/quake/
A software package to correct substitution sequencing errors in experiments with deep coverage (e.g. >15X), specifically intended for Illumina sequencing reads.
Proper citation: Quake (RRID:SCR_011839) Copy
Software providing a framework for collecting, storing, and accessing data produced by a wide variety of experiments.
Proper citation: SBEAMS (RRID:SCR_011830) Copy
A software package for visualizing data and information. It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions.
Proper citation: Circos (RRID:SCR_011798) Copy
http://www.h-invitational.jp/g-compass/
It visualizes evolutionarily conserved genomic regions between human and other 12 vertebrates based on original genome alignments pursuing higher coverage.
Proper citation: G-compass (RRID:SCR_011799) Copy
https://code.google.com/p/discovering-cse/
Software for discovering motifs that induce sequencing errors.
Proper citation: discovering-cse (RRID:SCR_011832) Copy
https://sites.google.com/site/moleculetagtoolbox/
A software package for building accurate ConSeqs from tagged reads.
Proper citation: MT-Toolbox (RRID:SCR_011833) Copy
http://ftp://ftp.pasteur.fr/pub/gensoft/projects/AlienTrimmer/
Allows detecting and removing multiple alien sequences in both ends of sequence reads.
Proper citation: AlienTrimmer (RRID:SCR_011835) Copy
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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