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http://www.ebi.ac.uk/ena/search/

A nucleotide sequence similiary search tool which is far faster than BLAST for large datasets, with only a marginal loss in search sensitivity.

Proper citation: ENA Sequence Search (RRID:SCR_013170) Copy   

•   Source: SciCrunch Registry

https://www.dandb.com/businessdirectory/precisionallograftsolutions-sanantonio-tx-5265368.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. A commercial tissue bank focusing on human tissue.

Proper citation: Precision Allograft Solutions (RRID:SCR_010702) Copy   

•   Source: SciCrunch Registry

http://www.asterand.com/

Provides human tissue for drug discovery scientists. * Human Biospecimens: Frozen & Fixed Human Tissues; Human RNA/DNA; Human Primary Cells / Cell lines; Custom Procurement; Oncology tissue, biofluid and RNA sets at special prices * Human Tissue-Based Services: Gene Expression, Molecular Pathology, Biochemical Pharmacology, Metabolism and Toxicity * Predictive Human Disease Models

Proper citation: Asterand (RRID:SCR_010703) Copy   

•   Source: SciCrunch Registry

http://www.benoslab.pitt.edu/comir/

Data analysis service that predicts whether a given mRNA is targeted by a set of miRNAs. ComiR uses miRNA expression to improve and combine multiple miRNA targets for each of the four prediction algorithms: miRanda, PITA, TargetScan and mirSVR. The composite scores of the four algorithms are then combined using a support vector machine trained on Drosophila Ago1 IP data.

Proper citation: ComiR (RRID:SCR_013023) Copy   

•   Source: SciCrunch Registry

http://trex.biohpc.org/

T-REX is a free, platform-independent online tool that allows for an integrated, rapid, and more robust analysis of T-RFLP data. Despite increasing popularity and improvements in terminal restriction fragment length polymorphism (T-RFLP) and other microbial community fingerprinting techniques, there are still numerous obstacles that hamper the analysis of these datasets. Many steps are required to process raw data into a format ready for analysis and interpretation. These steps can be time-intensive, error-prone, and can introduce unwanted variability into the analysis. Accordingly, we developed T-REX, free, online software for the processing and analysis of T-RFLP data. Analysis of T-RFLP data generated from a multiple-factorial study was performed with T-REX. With this software, we were able to i) label raw data with attributes related to the experimental design of the samples, ii) determine a baseline threshold for identification of true peaks over noise, iii) align terminal restriction fragments (T-RFs) in all samples (i.e., bin T-RFs), iv) construct a two-way data matrix from labeled data and process the matrix in a variety of ways, v) produce several measures of data matrix complexity, including the distribution of variance between main and interaction effects and sample heterogeneity, and vi) analyze a data matrix with the additive main effects and multiplicative interaction (AMMI) model.

Proper citation: T-REX (RRID:SCR_010715) Copy   

•   Source: SciCrunch Registry

http://comet.gobics.de/

A web-server for fast comparative functional profiling of metagenomes.

Proper citation: CoMet (RRID:SCR_011925) Copy   

•   Source: SciCrunch Registry

http://medicine.nus.edu.sg/tissue/

Tissue bank that provides samples and associated clinical information to associated researchers.

Proper citation: National University Tissue Repository (RRID:SCR_010717) Copy   

•   Source: SciCrunch Registry

http://www.textensor.com/

Textensor Limited specializes in software development and consulting related to interactive web based information management systems, web services, data modeling, and scientific computing. Our flagship product, a.nnotate.com, was launched in January 2008. It allows on-line review, annotation and discussion of web pages and a wide range of document types, including PDF and DOC, via a web browser. In April 2007 we launched PublicationsList.org to facilitate access to scientific research papers. It allows researchers to easily keep complete and reliable records of their research output on the web and gained more than 3000 users in the first 8 months. In 2005, Textensor won a SMART:Scotland award for a pilot study into techniques for authoring structured content from text. The first commercial product developed from this technology is a.nnotate.com. Recent consultancy clients include the University of Edinburgh for the development of PSICS, the Parallel Stochastic Ion Channel Simulator, the Okinawa Institute of Science and Technology for prototype code for stochastic diffusion, Memosyne Ltd for development of on-line memory tests for children, and Pearson Assessment for implementation of the Automated Working Memory Assessment.

Proper citation: Textensor Limited (RRID:SCR_010719) Copy   

•   Source: SciCrunch Registry

http://tools.genxpro.net/omiras/

A web server for the annotation, comparison and visualization of interaction networks of non-coding RNAs derived from small RNA-Sequencing experiments of two different conditions.

Proper citation: omiRas (RRID:SCR_010833) Copy   

•   Source: SciCrunch Registry

http://phylopythias.bifo.helmholtz-hzi.de/index.php?phase=wait

Web Server for Taxonomic Assignment of Metagenome Sequences that is a fast and accurate sequence composition-based classifier that utilizes the hierarchical relationships between clades. Taxonomic assignments with the web server can be made with a generic model, or with sample-specific models that users can specify and create. Several interactive visualization modes and multiple download formats allow quick and convenient analysis and downstream processing of taxonomic assignments.

Proper citation: PhyloPythiaS (RRID:SCR_011923) Copy   

•   Source: SciCrunch Registry

http://esharkgenome.imcb.a-star.edu.sg

To explore the elephant shark genome, we have conducted a survey-sequencing and comparative analysis of the elephant shark genome in collaboration with J. Craig Venter Institute. The elephant shark sequences generated under this project have been deposited at GenBank under the project accession number AAVX01000000. The sequences can also be searched using BLAST and retrieved here. Cartilaginous fishes (Chondrichthyes) represented by sharks, rays, skates and chimaeras, are phylogenetically the oldest group of living jawed vertebrates. They constitute an important group for our understanding of the origins of the complex developmental and physiological systems of jawed vertebrates. They are also an useful outgroup for bony vertebrates such as tetrapods and teleost fishes and help in identifying specialized features that have led to the evolution of diverse groups of bony vertebrates. The elephant shark (Callorhinchus milii), also known as the elephant fish and ghost shark, is a chimaera belonging to the Order Chimaeriformes and Family Callorhynchidae. It has the smallest genome among the known cartilaginous fish genomes. Thus, it was proposed as a model cartilaginous fish genome for whole-genome sequencing and comparative analysis (Venkatesh et al. 2005. Curr. Biol. 15: R82-R83). The following resources of the elephant shark are available for the scientific community: *Elephant Shark 1.4x assembly fasta sequences zipped 227 megabytes *Genomic DNA *~8x coverage BAC library (average insert size, ~150 kb) *cDNA libraries (under construction) *cDNA (dated 11 April 2008) with orthologs in 5 vertebrates (human, opossum, chicken, frog, fugu)

Proper citation: Elephant shark genome sequencing (RRID:SCR_013158) Copy   

•   Source: SciCrunch Registry

http://compbio.med.harvard.edu/CGHweb/

Data analysis service enabling users to analyse their array-CGH data with multiple algorithms simultaneously.

Proper citation: CGHweb (RRID:SCR_010923) Copy   

•   Source: SciCrunch Registry

http://gsgator.ewha.ac.kr/

A web-based platform for functional interpretation of gene sets with features such as cross-species Gene Set Analysis (GSA), Flexible and Interactive GSA, simultaneous GSA for multiple gene set, and and a fully integrated network viewer for both visualizing GSA results and molecular networks.

Proper citation: gsGator (RRID:SCR_012035) Copy   

•   Source: SciCrunch Registry

http://agvgd.iarc.fr/index.php

A freely available, web-based program that combines the biophysical characteristics of amino acids and protein multiple sequence alignments to predict where missense substitutions in genes of interest fall in a spectrum from enriched delterious to enriched neutral.

Proper citation: Align-GVGD (RRID:SCR_010772) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/specimen-bank-bwh-harvard

Core facility that provides the following services: Open repositories service, Sample processing service, Medical/pathology informatics support service, BWH tissue repository service.

The Specimen Bank provides materials to investigators with IRB-approved protocols. Staff are available to assist with selection of samples appropriate for downstream applications, development of processing protocols or preparation of derivatives from clinical materials. IT Staff are also available to assist researchers with creation of queries for prospective sample collection or queries to select samples from specific cohorts. Their goal is to drive quality research in an efficient and cost-effective manner. Each year they provide tens of thousands of samples to area researchers. Getting started: Partners investigators and study staff may request a Crimson user account to help manage studies and collected materials.

Proper citation: BWH Specimen Bank (RRID:SCR_012316) Copy   

•   Source: SciCrunch Registry

http://www.mutationtaster.org/

Evaluates disease-causing potential of sequence alterations.

Proper citation: MutationTaster (RRID:SCR_010777) Copy   

•   Source: SciCrunch Registry

http://hyperbrowser.uio.no/hb/

A generic web-based system, providing statistical methodology and computing power to handle a variety of biological inquires on genomic datasets.

Proper citation: Genomic HyperBrowser (RRID:SCR_010909) Copy   

•   Source: SciCrunch Registry

https://genome-cancer.ucsc.edu/

A suite of web-based tools to visualize, integrate and analyze cancer genomics and its associated clinical data. It is possible to display your own clinical data within one of their datasets.

Proper citation: UCSC Cancer Genomics Browser (RRID:SCR_011796) Copy   

•   Source: SciCrunch Registry

http://lablog.sourceforge.net

An ELN (electronic lab notebook) software application which can be used to document neuroscience projects and store metadata. LabLog is meant to constitute a laboratory's long term memory for project related information. To do this, project information is stored in a central laboratory database and can be easily retrieved by searching and filtering.

Proper citation: LabLog (RRID:SCR_013975) Copy   

•   Source: SciCrunch Registry

http://weizhong-lab.ucsd.edu/metagenomic-analysis/

A customizable web server for fast metagenomic analysis.

Proper citation: WebMGA (RRID:SCR_011951) Copy   

•   Source: SciCrunch Registry