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http://www.nipgr.res.in/ngsqctoolkit.html

A software toolkit for the quality control (QC) of next generation sequencing (NGS) data. The toolkit comprises of user-friendly stand alone tools for quality control of the sequence data generated using Illumina and Roche 454 platforms with detailed results in the form of tables and graphs, and filtering of high-quality sequence data. It also includes few other tools, which are helpful in NGS data quality control and analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: NGS QC Toolkit (RRID:SCR_005461) Copy   

•   Source: SciCrunch Registry

http://mta.hu/english/

The Hungarian Academy of Sciences is the most important and prestigious learned society of Hungary. Its seat is at the bank of the Danube in Budapest, between Széchenyi rakpart and Akadémia utca.

Proper citation: Hungarian Academy of Sciences; Budapest; Hungary (RRID:SCR_005654) Copy   

•   Source: SciCrunch Registry

http://neuromorphometrics.com

Neuromorphometrics provides brain labeling and measurement services. Given raw MRI brain scans, we make precise quantitative measurements of the volume, shape, and location of specific neuroanatomical structures. Web tool for brain measurement services. Used for modeling living human brain and make quantitative measurements of volume, shape, and location of specific neuroanatomical structures using given MRI brain scans. Automated analyses are manually guided, inspected and certified by a neuroanatomical expert. Resource of neuroanatomically labeled MRI brain scans database. Resource for neuroanatomical localization and identification: NeuAtlas.

Proper citation: Neuromorphometrics (RRID:SCR_005656) Copy   

•   Source: SciCrunch Registry

http://www.phrap.org/consed/consed.html

A graphical tool for sequence finishing (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit, and Align Reads To Reference Sequence)

Proper citation: Consed (RRID:SCR_005650) Copy   

•   Source: SciCrunch Registry

http://www.chemnavigator.com/cnc/services/SCSORS_Overview.asp

ChemNavigator has extended its agreement with NCI to include the development of a new Semi-Custom Synthesis On-line Request System (SCSORS), funded mostly by NCI with additional financial support from the NIH Chemical Genomics Center (NCGC). The new SCSORS project will provide the NIH access to the world''s supply of synthetic chemistry available for drug discovery. Once fully formed, SCSORS will provide a strategy for all NIH scientists to circulate requests for specific chemical samples among thousands, if not tens of thousands, of synthetic chemists at suppliers registered in the system. Sample quantities will range from milligram up to kilogram scale requests. Suppliers will be provided tools that allow them to review these requests and make proposals to NIH scientists for the synthesis of substances. It is expected that using the SCSORS strategy will allow the NIH to acquire chemical samples at less than 10% of the internal cost of synthesis while offering access to world wide chemical expertise and diversity. Once fully implemented, SCSORS will become an archive of commercially accessible custom chemistry products for pharmaceutical research. It is expected that this database of commercially accessible substances will grow to over 250 million substances in the coming two years.

Proper citation: SCSORS - Semi-Custom Synthesis On-line Request System (RRID:SCR_005636) Copy   

•   Source: SciCrunch Registry

http://ngsview.sourceforge.net/

A generally applicable, flexible and extensible next-generation sequence alignment editor. The software allows for visualization and manipulation of millions of sequences simultaneously on a desktop computer, through a graphical interface.

Proper citation: NGSView (RRID:SCR_005637) Copy   

•   Source: SciCrunch Registry

http://cgap.nci.nih.gov/Genes/GOBrowser

With the CGAP GO browser, you can browse through the GO vocabularies, and find human and mouse genes assigned to each term. GO data updated every few months. Platform: Online tool

Proper citation: CGAP GO Browser (RRID:SCR_005676) Copy   

•   Source: SciCrunch Registry

http://vortex.cs.wayne.edu/projects.htm#Onto-Express

The typical result of a microarray experiment is a list of tens or hundreds of genes found to be differentially regulated in the condition under study. Independently of the methods used to select these genes, the common task faced by any researcher is to translate these lists of genes into a better understanding of the biological phenomena involved. Currently, this is done through a tedious combination of searches through the literature and a number of public databases. We developed Onto-Express (OE) as a novel tool able to automatically translate such lists of differentially regulated genes into functional profiles characterizing the impact of the condition studied. OE constructs functional profiles (using Gene Ontology terms) for the following categories: biochemical function, biological process, cellular role, cellular component, molecular function and chromosome location. Statistical significance values are calculated for each category. We demonstrated the validity and the utility of this comprehensive global analysis of gene function by analyzing two breast cancer data sets from two separate laboratories. OE was able to identify correctly all biological processes postulated by the original authors, as well as discover novel relevant mechanisms (Draghici et.al, Genomics, 81(2), 2003). Other results obtained with Onto-Express can be found in Khatri et.al., Genomics. 79(2), 2002. Custom level of abstraction of the Gene Ontology. User account required. Platform: Online tool

Proper citation: Onto-Express (RRID:SCR_005670) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/bsmap/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18,2023. Short reads mapping software for bisulfite sequencing reads.

Proper citation: BSMAP (RRID:SCR_005671) Copy   

•   Source: SciCrunch Registry

http://www.genetools.us

Web-service providing access to database that brings together information from broad range of resources. Web application for functional annotation and statistical hypothesis testing. Provides tools for analysis of genomic and microarray data. Collection of tools include Bibliographic Information,Databases,Gene Annotation,Gene Regulation, Microarray,Proteins,Sequence Manipulation - Nucleic Acids,Sequence Manipulation - Protein, Systems Biology.

Proper citation: GeneTools (RRID:SCR_005663) Copy   

•   Source: SciCrunch Registry

http://www.webarraydb.org/webarray/index.html

An open source integrated microarray database and analysis suite that features convenient uploading of data for storage in a MIAME (Minimal Information about a Microarray Experiment) compliant fashion. It allows data to be mined with a large variety of R-based tools, including data analysis across multiple platforms. Different methods for probe alignment, normalization and statistical analysis are included to account for systematic bias. Student's t-test, moderated t-tests, non-parametric tests and analysis of variance or covariance (ANOVA/ANCOVA) are among the choices of algorithms for differential analysis of data. Users also have the flexibility to define new factors and create new analysis models to fit complex experimental designs. All data can be queried or browsed through a web browser. The computations can be performed in parallel on symmetric multiprocessing (SMP) systems or Linux clusters.

Proper citation: WebArrayDB (RRID:SCR_005577) Copy   

•   Source: SciCrunch Registry

http://biostat.mc.vanderbilt.edu/wiki/Main/ASAP

Software developed to provide a framework for building and executing a pipeline to preprocess next generation sequence data and variant calls.

Proper citation: Advanced Sequence Automated Pipeline (RRID:SCR_005578) Copy   

•   Source: SciCrunch Registry

http://samtools.sourceforge.net/tview.shtml

Text alignment viewer software based on the GNU ncurses library that works with short indels and shows MAQ consensus. It uses different colors to display mapping quality or base quality, subjected to users' choice.

Proper citation: SAMtools Text Alignment Viewer (RRID:SCR_005611) Copy   

•   Source: SciCrunch Registry

http://fields.scripps.edu/

Scientists at the Yates Lab at The Scripps Research Institute (TSRI) rely on information yielded by tandem mass spectrometry to identify proteins from complex mixtures. Using this powerful technique, researchers draw upon a cross section of fields to increase the scope, sensitivity, and throughput of technologies for practical proteomics. Biologists provide the questions that drive our research. By identifying complexes that are poorly understood or organism-wide issues requiring further exploration, we gain a theoretical understanding of issues that are tractable only through proteomic strategies. Analytical chemists and biochemists improve our tools for revealing the proteins present in biological samples. Targets for optimization include the isolations used to obtain proteins, the steps to generate peptides from these proteins, and the separation of peptides en route to the mass spectrometer. Chemistry is vital to increasing power of proteomic technology. Computer science yields tools on two scales. First, the sequence corresponding to each peptide''s tandem mass spectrum must be identified. Once those identifications have been completed, additional tools are needed to summarize and organize these identifications.

Proper citation: TSRI-Yates Lab (RRID:SCR_005699) Copy   

•   Source: SciCrunch Registry

http://www.georgetown.edu/

Georgetown University is a private research university in the Georgetown neighborhood of Washington, D.C. The oldest Catholic and Jesuit institution of higher education in the United States.

Proper citation: Georgetown University; Washington D.C.; USA (RRID:SCR_005575) Copy   

•   Source: SciCrunch Registry

http://compbio.clemson.edu/index.html

The research in the lab focuses on computational modeling of biological macromolecules and their assemblages and predicting biophysical quantities associated with them. The main focus of the lab is the development and maintenance of the popular software package DelPhi, which calculates electrostatic potential and energies of systems comprised of biological macromolecules. In addition, we are interested in modeling disease-causing missense mutations, pKa''s of amino acids and nucleic groups and pH-dependence of stability and binding. In parallel with in silico modeling, the lab actively collaborates with experimetalists to better understand molecular mechanisms of biological reactions and interactions. The combination of the methods of Computational Biophysics and Bioinformatics with experimental results is an essential approach utilized in our research.

Proper citation: Clemson Computational Biophysics and Bioinformatics (RRID:SCR_005696) Copy   

•   Source: SciCrunch Registry

http://cs.nyu.edu/~bingsun/

NYU Bioinformatics group applies algorithmic, statistical, and mathematical techniques to solve problems of interest to biology, biotechnology and biomedicine. The group focuses on bioinformatics, computational biology and systems biology with many active projects in areas ranging from single molecules to entire populations: Analysis of Single-Molecule/Single-Cell Data, SPM-based Transcriptomic Profiling, Whole-Genome Haplotype Sequencing using SMASH (Single Molecule Approaches to Haplotype Sequencing), SUTTA (Scoring and Unfolding Trimmed Tree Assembler) assembly algorithm, Analysis of Spatio-Temporal Data, Model Checking and Model Building for Systems Biology, GOALIE-based Phenomenological Models and their Verification, Causality Analysis, Causal Models and their Verification, Analysis of EHR (Electronic Health Record Data) and Disease Models (e.g., Chronic Fatigue Syndrome, Congestive Heart Failure, Deep Vein Thrombosis, etc.), Models of Cancer, Applications to Pancreatic Cancer, Polymorphisms and Biomarkers, Strategies for Group Testing, Epidemiological and Bio-Warfare Models, Planning with Large Agent Networks against Catastrophes (PLAN C), Population Genomics, and Genome Wide Association Studies (GWAS). The group has received its funding from Air Force, Army, CCPR, DARPA, NIH, NIST, NSF, NYSTAR, etc. and various other governmental and commercial entities. Currently, the group is part of an NSF funded Expedition in Computing project (CMACS: Center for Modeling and Analysis of Complex Systems at CMU) and collaborates widely, both nationally and internationally. The group is highly multi-disciplinary, attracting researchers and students from mathematics, statistics, computer science, and biology who team up with physicians, physicists, and chemists as well as professionals in their own disciplines. This group is led by Prof. Bud Mishra, a professor of computer science and mathematics at NYU''s Courant Institute of Mathematical Sciences.

Proper citation: NYU Bioinformatics Group (RRID:SCR_005697) Copy   

•   Source: SciCrunch Registry

https://www.jax.org/jax-mice-and-services/in-vivo-pharmacology/neurobiology-services

A laboratory that researches neurological diseases, including amyotrophic lateral sclerosis, Alzheimer's disease, glaucoma, retinitis pigmentosa, epilepsy, and hearing disorders. The Laboratory offers courses that train and update neuroscience researchers. It distributes JAX Mice models suitable for neuroscience research. Also available are research tools for neurobiology.

Proper citation: Jackson Laboratory Neurobiology (RRID:SCR_005570) Copy   

•   Source: SciCrunch Registry

http://rafalab.jhsph.edu/bsmooth/

A pipeline for analyzing whole genome bisulfite sequencing (WGBS) data.

Proper citation: BSmooth (RRID:SCR_005693) Copy   

•   Source: SciCrunch Registry

http://cre.jax.org/index.html

Repository of Cre Driver lines and related information resources. Their services include analysis of Cre line excision function in both target and non-target tissues using Cre reporter lines and presenting the annotated data in the expression data portion of this website, http://cre.jax.org/data.html.

Proper citation: JAX Cre Repository (RRID:SCR_005566) Copy   

•   Source: SciCrunch Registry