Tools   Select Another Resource Report Type

http://www.nitrc.org/projects/meshmetric3d/

Software visualization tool based on the VTK library. Its main feature is to measure and display surface-to-surface distance between two triangle meshes using user-specified uniform sampling. Offers all the basic tools to visualize meshes such as color, opacity, smoothing, down sampling or type of representation.

Proper citation: 3DMeshMetric (RRID:SCR_000043) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/ontomorphtab/

OntoMorph is a tab plugin for Protege-OWL 3 that allows a user to mark-up portions of a Neurolucida neuron morphology with OWL instances. A user loads a Neurolucida morphology file, either from their hard drive or from an arbitrary URL, into an interface that allows them to zoom, rotate, and translate the morphology. The interface allows them to select points on the morphology to indicate points, segments, or subtrees of the morphology they wish to assign to an OWL instance. After this selection has been made, OntoMorph saves the selection to the currently active OWL instance in the ontology that is currently loaded into Protege. No modifications are made to the Neurolucida file itself. As a result, an association is created between that portion of the morphology and the OWL instance, such that selecting the OWL instance allows retrieval of the portion. Upon retrieval, the morphology portion can be highlighted, so the user can keep track of what pieces each instance refer to.

Proper citation: OntoMorph Tab (RRID:SCR_000443) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/gmato/files/?source=navbar

A software tool used for simple sequence repeats (SSR) or microsatellite characterization. It also facilitates SSR marker design on a genomic scale, microsatellite mining at any length, and comprehensive statistical analysis for DNA sequences in any genome at any size. Analysis parameters are customizable.

Proper citation: GMATo (RRID:SCR_000165) Copy   

•   Source: SciCrunch Registry

https://trialweb.dcri.duke.edu/tads/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Multi-site clinical research study examining the short- and long-term effectiveness of an antidepressant medication and psychotherapy alone and in combination for treating depression in adolescents ages 12 to 17. For teens treated in TADS, the trial is designed to provide best-practice practical care for depression.

Proper citation: TADS - Treatment for Adolescents with Depression Study (RRID:SCR_000037) Copy   

•   Source: SciCrunch Registry

http://www.incf.org/resources/data-space/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented August 21, 2017.

Repository for sharing of neuroscience data, text, images, sounds, movies, models and simulations.

Proper citation: INCF Dataspace (RRID:SCR_000158) Copy   

•   Source: SciCrunch Registry

http://gst.tennessee.edu/

Graduate School of Genome Science and Technology (GST) is a Life Science graduate program founded on two premises. First, whole-genome sequences and related large-scale datasets have transformed how we perform biological research, a trend that is gathering momentum and is anticipated to frame the way the biology research is accomplished for many years to come. Second, advances in technology, whether at the level of instrumentation, computation, or wet lab reagents, have long been a powerful driving force in biology. The GST program is home to faculty mentors from many walks of life. The virulence factors of pathogenic fungi and the engineering of photosynthetic reaction complexes for bioenergy harvesting are just two examples from the cornucopia of research projects being pursued in GST.

Proper citation: University of Tennessee Genome Science and Technology Graduate Program (RRID:SCR_000038) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/rnaseqvariantbl/

Open source software tool that simulates experimental RNA-seq and DNA whole exome sequences derived from reference genome, aligns these sequences by custom parameters, detects variants and outputs blacklist of positions and alleles caused by mismapping. Used to characterize mappability of RNA-Seq reads and create blacklist of genomic positions of mismapped reads. This blacklist is used to filter potential false positives from variant or RNA editing calls.

Proper citation: BlackOPs (RRID:SCR_000032) Copy   

•   Source: SciCrunch Registry

http://onlinelibrary.wiley.com/journal/10.1002/%28ISSN%291757-7012

Wiley Interdisciplinary Reviews series combines features of encyclopedic reference works and review journals in innovative online format. They are designed to promote cross-disciplinary research ethos while maintaining the highest scientific and presentational standards, but should be viewed first and foremost as evolving online databases of cutting-edge reviews.

Proper citation: WILEY Interdisciplinary Reviews (RRID:SCR_000392) Copy   

•   Source: SciCrunch Registry

http://sw-tools.pdb.org/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Information Portal to Biological Macromolecular Structures provides variety of software tools made available through the RCSB. These tools include: data extraction and deposition preparation tools, data format conversion and validation tools, data parsing tools, dictionary and data management tools, visualization tools that support PDBx/mmCIF, and other PDBx/mmCIF software library tools.

Proper citation: RCSB PDB Software Tools (RRID:SCR_000035) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/DESeq.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Software for differential gene expression analysis based on the negative binomial distribution. It estimates variance-mean dependence in count data from high-throughput sequencing assays and tests for differential expression.

Proper citation: DESeq (RRID:SCR_000154) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/popbam/

A tool to perform evolutionary or population-based analyses of next-generation sequencing data. POPBAM takes a BAM file as its input and can compute many widely used evolutionary genetics measures in sliding windows across a genome.

Proper citation: POPBAM (RRID:SCR_000464) Copy   

•   Source: SciCrunch Registry

https://www.schrodinger.com/glide

Software package which approximates a complete search of the conformational, orientational, and positional space of the ligand in a given receptor. Used in drug development for predicting protein ligand binding modes and ranking ligands via high throughput virtual screening.

Proper citation: Glide (RRID:SCR_000187) Copy   

•   Source: SciCrunch Registry

http://www.unavco.org/data/web-services/documentation/unavco-ws-api/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Web services to access UNAVCO data collection. Adding /gps, /met, /pore, /tilt, and /strain gives the sensor JSON description.

Proper citation: UNAVCO Geodetic Web Services (RRID:SCR_000181) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/gasv/

Software tool for identifying structural variants (SVs) from paired-end sequencing data.GASV distribution includes three components that are typically run in succession: the BAM file of unique paired-read mappings is processed; structural variants are identified by clustering discordant fragments; and a probabilistic algorithm improves the specificity of GASV predictions.

Proper citation: GASV (RRID:SCR_000061) Copy   

•   Source: SciCrunch Registry

https://github.com/brantp/rtd

Reference-free ddRADseq analysis software tools. The pipeline script generates reference-sorted, indexed BAM from uniqued reads from radtag sequencing lanes.

Proper citation: rtd (RRID:SCR_000337) Copy   

•   Source: SciCrunch Registry

http://www.cdisc.org/

A global, open, multidisciplinary, non-profit organization that has established standards to support the acquisition, exchange, submission and archive of clinical research data and metadata. Its mission is to develop and support global, platform-independent data standards that enable information system interoperability to improve medical research and related areas of healthcare. CDISC standards are vendor-neutral, platform-independent and freely available via the CDISC website.

Proper citation: Clinical Data Interchange Standards Consortium (RRID:SCR_000219) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/chipmeta/

Software using a Hierarchical hidden Markov model for jointly analyzing ChIP-chip and ChIP-seq datasets.

Proper citation: ChIPmeta (RRID:SCR_000054) Copy   

•   Source: SciCrunch Registry

https://www.infoquant.com/oneclickcgh

Platform-independent array copy number analysis software that provides straightforward yet comprehensive detection and reporting of copy number changes.

Proper citation: oneClickCGH (RRID:SCR_000294) Copy   

•   Source: SciCrunch Registry

http://knightadrc.wustl.edu/

The Charles F. and Joanne Knight Alzheimer Disease Research Center (Knight ADRC) supports researchers and our surrounding community in their pursuit of answers that will lead to improved diagnosis and care for persons with Alzheimer disease (AD). The Center is committed to the long-term goal of finding a way to effectively treat and prevent AD. The Knight ADRC facilitates advanced research on the clinical, genetic, neuropathological, neuroanatomical, biomedical, psychosocial, and neuropsychological aspects of Alzheimer disease, as well as other related brain disorders.

Proper citation: Washington University School of Medicine Knight Alzheimers Disease Research Center (RRID:SCR_000210) Copy   

•   Source: SciCrunch Registry

http://fiduswriter.org/

An online collaborative editor for academics that use citations and/or formulas. The editor focuses on the content rather than the layout, so that with the same text, it can be published in multiple ways: On a website, as a printed book, or as an ebook.

Proper citation: Fiduswriter (RRID:SCR_000204) Copy   

•   Source: SciCrunch Registry