Tools   Select Another Resource Report Type

http://mendel.stanford.edu/SidowLab/downloads/gerp/

Software that identifies constrained elements in multiple alignments by quantifying substitution deficits. These deficits represent substitutions that would have occurred if the element were neutral DNA, but did not occur because the element has been under functional constraint. We refer to these deficits as Rejected Substitutions. Rejected substitutions are a natural measure of constraint that reflects the strength of past purifying selection on the element. GERP estimates constraint for each alignment column; elements are identified as excess aggregations of constrained columns. A false-positive rate (which is user-settable) is calculated using "shuffled" alignments in which the order of columns is randomized., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GERP (RRID:SCR_000563) Copy   

•   Source: SciCrunch Registry

https://www.noldus.com/ethovision

Video tracking software that tracks and analyzes the behavior, movement, and activity of any animal.

Proper citation: EthoVision XT (RRID:SCR_000441) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/cancer/cga/mutect

Software for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.

Proper citation: MuTect (RRID:SCR_000559) Copy   

•   Source: SciCrunch Registry

http://hypothes.is/

Non-profit organization working towards developing an open platform for the collaborative evaluation of knowledge. It will combine sentence-level critique with community peer-review to provide commentary, references, and insight on top of news, blogs, scientific articles, books, terms of service, ballot initiatives, legislation and regulations, software code and more.

Proper citation: Hypothes.is (RRID:SCR_000430) Copy   

•   Source: SciCrunch Registry

http://thomsonreuters.com/metadrug/

A leading systems pharmacology solution that incorporates extensive manually curated information on biological effects of small molecule compounds. Predictive and analytical algorithms look at chemical compounds from different angles in one integrated workflow are available for: * Individual previously described compounds to look up their known information and predict currently unknown properties * Individual newly synthesized or isolated compounds to predict their properties from its structures * Compound libraries to extract known and predict new properties of individual compounds and perform their comparison and prioritization

Proper citation: MetaDrug (RRID:SCR_000461) Copy   

•   Source: SciCrunch Registry

https://mulcyber.toulouse.inra.fr/plugins/mediawiki/wiki/ng6/index.php/Pyrocleaner

A software module for cleaning 454 pyrosequencing reads using filters such as read duplication, length, complexity, base-pair quality and number of undetermined bases. The software also uses flowgram files of paired-end sequences to validate paired-ends files of another file.

Proper citation: Pyrocleaner (RRID:SCR_000584) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/GeneExpressionSignature.html

An R package developed for the large-scale analysis of gene expression signatures. It gives the implementations of the gene expression signature and its distance to each. Gene expression signature is represented as a list of genes whose expression is correlated with a biological state of interest. And its distance is defined using a nonparametric, rank-based pattern-matching strategy based on the Kolmogorov-Smirnov statistic. Gene expression signature and its distance can be used to detect similarities among the signatures of drugs, diseases, and biological states of interest.

Proper citation: GeneExpressionSignature (RRID:SCR_000455) Copy   

•   Source: SciCrunch Registry

http://regenbase.org

Information framework and knowledge base to facilitate research about nervous system regeneration. It includes minimal information standards, an ontology that is linked to other ontologies, and a knowledge base built with a triple store and a relational database.

Proper citation: RegenBase (RRID:SCR_000456) Copy   

•   Source: SciCrunch Registry

https://www.openmicroscopy.org/site/products/bio-formats

Standalone software Java library for reading microscopy image data files in any format and writing image data using standardized, open formats. It currently reads and converts more than 120 file formats to the OME-TIFF data standard.

Proper citation: Bio-Formats (RRID:SCR_000450) Copy   

•   Source: SciCrunch Registry

http://wannovar.usc.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Web interface to the ANNOVAR software, a tool to annotate functional consequences of genetic variation from high-throughput sequencing data, to help biologists without bioinformatics skills to easily submit a list of mutations (even whole-genome variants calls) to the web server, select the desired annotation categories, and receive functional annotation back by emails. Given a list of single nucleotide variants (SNVs) and insertions / deletions in VCF or ANNOVAR input format, wANNOVAR annotates their functional effects on genes (such as amino acid changes for non-synonymous SNPs), calculate their predicted functional importance scores (such as SIFT and PolyPhen scores), retrieve allele frequencies in public databases (such as the 1000 Genomes Project and NHLBI-ESP 6500 exomes), and implement a variants reduction protocol to identify a subset of potentially deleterious variants., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: wANNOVAR (RRID:SCR_000565) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/virema/

Software Python package for detection, alignment and reporting of recombination events in Next-Generation Sequencing data. Detects and reports recombination or fusion events in virus genomes using deep sequencing datasets.

Proper citation: ViReMa (RRID:SCR_000566) Copy   

•   Source: SciCrunch Registry

http://www.Ablynx.com

A biopharmaceutical company engaged in the discovery and development of Nanobodies, a novel class of antibody-derived therapeutic proteins based on single-domain antibody fragments, for a range of serious life-threatening human diseases including inflammation, hematology, oncology and pulmonary disease.

Proper citation: Ablynx (RRID:SCR_002940) Copy   

•   Source: SciCrunch Registry

http://www.ataxia.org/

Membership supported, nonprofit organization established dedicated to improving the lives of persons affected by ataxia through support, education, and research. The Foundation's primary purpose is to support promising ataxia research and to provide vital programs and services for ataxia families. The Foundation first began direct funding of ataxia research through the NAF Research Seed-Money Program. Since that time, the Foundation has established additional research programs which have included programs such as the NAF Young Investigator Award, the NAF Fellowship Award and other research initiatives. NAF research programs continue to fund promising ataxia research studies throughout the world. The Foundation supports research in dominant ataxia (including SCAs), recessive ataxia (including Friedreich's) and sporadic ataxia. The Foundation has developed an extensive library of NAF brochures, fact sheets, books, and videos on ataxia. Also available to its members is the Foundation's quarterly news publication, Generations. This 48 page ataxia news magazine provides the latest information on ataxia research, articles on living with ataxia, personal accounts from ataxia families throughout the United States, and much more.

Proper citation: National Ataxia Foundation (RRID:SCR_002933) Copy   

•   Source: SciCrunch Registry

http://www.schizophreniaforum.org/

The mission of the SRF is to help in the search for causes, treatments, and understanding of the devastating disease of schizophrenia. Our goal is to foster collaboration among researchers by providing an international online forum where ideas, research news, and data can be presented and discussed. The website is intended to bring together scientists working specifically on schizophrenia, scientists researching related diseases, and basic scientists whose work can shed light on these diseases. In this way, we hope that the Schizophrenia Research Forum will be a catalyst for creative thinking in the quest to understand a deeply complex disease. It is our goal to create and maintain up-to-date content of the highest quality. The website is free of charge to users, independent of industry sponsorship, and open to the public. Though geared toward researchers, we welcome other visitorspeople with mental illnesses, families, the media, and others who need accurate information on research into schizophrenia. We do, however, require that users who wish to post comments and other materials be registered members. All such materials are subject to approval by the editorial team. As a forum, we encourage participation and welcome feedback from the community.

Proper citation: Schizophrenia Research Forum (RRID:SCR_002899) Copy   

•   Source: SciCrunch Registry

http://microcal-origin.software.informer.com/

A complete graphing and data analysis software package that provides a suite of features catering to the needs of scientists and engineers. Main features: * Drag-and-drop import of data and images * Save import settings to a worksheet or external files for repeated use * Use saved settings to re-import files with a single click * Post-process imported data * Import Wizard with visual feedback * Handle non-standard files by programming

Proper citation: Microcal Origin (RRID:SCR_002815) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/devel/bioc/html/CGHnormaliter.html

Software for normalization and centralization of array comparative genomic hybridization (aCGH) data with imbalanced aberrations. The algorithm uses an iterative procedure that effectively eliminates the influence of imbalanced copy numbers. This leads to a more reliable assessment of copy number alterations (CNAs).

Proper citation: CGHnormaliter (RRID:SCR_002936) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/Software/MBAT

Workflow environment bringing together heterogenous, online biological image resources, a user's image data and biological atlases in a concise, unified and intuitive workspace. The MBAT viewer displays multiple images on a single virtual canvas allowing easy side-by-side comparisons and image compositing. MBAT is written in Java so it is platform independent and is highly extensible through it's plugin architecture. MBAT integrates three distinct workspaces for online search, image alignment (registration) and image display: * Search Workspace: able to submit a query to multiple databases simultaneously and online literature searches. * Registration Workspace: performs 2D landmark based registration. * Viewer Workspace: displays & composites images and image volumes using high performance graphics hardware. * Atlas Viewer: allows navigation and interrogation of volumetric atlases. * Hierarchy Editor: create logical groupings of atlas labels.

Proper citation: Mouse BIRN Atlasing Toolkit (RRID:SCR_002814) Copy   

•   Source: SciCrunch Registry

http://www.training.nih.gov/

Division of the Office of Intramural Research (OIR), Office of the Director (OD) which provides services to current trainees in programs in the NIH Intramural Research Program, potential applicants to training programs at the NIH, investigators and staff at the NIH, and trainees and investigators outside the NIH.

Proper citation: Office of Intramural Training and Education (RRID:SCR_002934) Copy   

•   Source: SciCrunch Registry

http://www.hgsc.bcm.tmc.edu/content/honey-bee-genome-project

The HGSC has sequenced the honey bee, Apis mellifera. The version 4.0 assembly was released in March 2006 and published in October 2006. The genome sequence is being upgraded with additional sequence coverage. The honey bee is important in the agricultural community as a producer of honey and as a facilitator of pollination. It is a model organism for studying the following human health issues: immunity, allergic reaction, antibiotic resistance, development, mental health, longevity and diseases of the X chromosome. In addition, biologists are interested in the honey bee's social organization and behavioral traits. This project was proposed to the HGSC by a group of dedicated insect biologists, headed by Gene Robinson. Following a workshop at the HGSC and a honey bee white paper, the HGSC began the project in 2002. A 6-fold coverage WGS, BAC sequence from pooled arrays, and an initial genome assembly (Amel_v1.0) were released beginning in 2003. This has been a challenging project with difficulty in recovering AT-rich regions. The WGS data had lower coverage in AT-rich regions and BAC data from clones showed evidence of internal deletions. Additional reads from AT enriched DNA addressed these underrepresented regions. The current assembly Amel_4.0 was produced with Atlas and includes 2.7 million reads (1.8 Gb) or 7.5x coverage of the (clonable) genome. About 97% of STSs, 98% of ESTs, and 96% of cDNAs are represented in the 231 Mb assembly. About 2,500 reads were also produced from a strain of Africanized honey bee and SNPs were extracted. These were released in dbSNP and the NCBI Trace Archive. Analysis of the genome by a consortium of 20 labs has been completed. This produced a gene list derived from five different methods melded through the GLEAN software. Publications include a main paper in Nature and up to forty companion papers in Genome Research and Insect Molecular Biology. Sponsors: Sequencing of the honey bee is jointly funded by National Human Genome Research Institute (NHGRI) and the Department of Agriculture (USDA). Multiple drones from the same queen (strain DH4) were obtained from Danny Weaver of B. Weaver Apiaries. All libraries were made from DNA isolated from these drones. The honey bee BAC library (CHORI-224) was prepared by Pieter de Jong and Katzutoyo Osoegawa at the Children's Hospital Oakland Research Institute.

Proper citation: Honey Bee Genome Project (RRID:SCR_002890) Copy   

•   Source: SciCrunch Registry

http://neuinfo.org

Framework for identifying, locating, relating, accessing, integrating, and analyzing information from neuroscience research. Users can search for and add neuroscience-related resources at NIF portal and receive and RRID to track and cite resources within scientific manuscripts.

Proper citation: Neuroscience Information Framework (RRID:SCR_002894) Copy   

•   Source: SciCrunch Registry