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http://blast.ncbi.nlm.nih.gov/Blast.cgi

Web search tool to find regions of similarity between biological sequences. Program compares nucleotide or protein sequences to sequence databases and calculates statistical significance. Used for identifying homologous sequences.

Proper citation: NCBI BLAST (RRID:SCR_004870) Copy   

•   Source: SciCrunch Registry

http://www.nlm.nih.gov/mesh

A controlled vocabulary thesaurus that consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. MeSH, in machine-readable form, is provided at no charge via electronic means. MeSH descriptors are arranged in both an alphabetic and a hierarchical structure. At the most general level of the hierarchical structure are very broad headings such as Anatomy or Mental Disorders. More specific headings are found at more narrow levels of the twelve-level hierarchy, such as Ankle and Conduct Disorder. There are 27,149 descriptors in 2014 MeSH. There are also over 218,000 entry terms that assist in finding the most appropriate MeSH Heading, for example, Vitamin C is an entry term to Ascorbic Acid. In addition to these headings, there are more than 219,000 headings called Supplementary Concept Records (formerly Supplementary Chemical Records) within a separate thesaurus. The MeSH thesaurus is used by NLM for indexing articles from 5,400 of the world''''s leading biomedical journals for the MEDLINE/PubMED database. It is also used for the NLM-produced database that includes cataloging of books, documents, and audiovisuals acquired by the Library. Each bibliographic reference is associated with a set of MeSH terms that describe the content of the item. Similarly, search queries use MeSH vocabulary to find items on a desired topic.

Proper citation: MeSH (RRID:SCR_004750) Copy   

•   Source: SciCrunch Registry

http://www.startthecure.com/

South Texas Accelerated Research Therapeutics (START) directs clinical trials of novel anticancer agents using a high quality and innovative information technology infrastructure to ensure accurate and rapid clinical trials in a setting that emphasizes personalized and compassionate clinical care. START''s head office is located in San Antonio, Texas, in the heart of the South Texas Medical Center. With centers located in San Antonio, Texas and Madrid, Spain, START conducts the world''s largest Phase I medical oncology program putting more than 400 patients per year on Phase I trials. Patients travel from all over the world to participate in one or more of our Phase I drug trials. START consists of a team of highly trained physicians and staff with extensive experience in Phase I clinical trials research and are nationally recognized as thought leaders in cancer research and drug development. The mission of START is to accelerate the development of new anticancer drugs that will improve the quality of life and survival for patients with cancer. Our drug development program is not only furthering cancer research, but also offers hope to patients facing the toughest cancer battles.

Proper citation: South Texas Accelerated Research Therapeutics (RRID:SCR_004867) Copy   

•   Source: SciCrunch Registry

http://www.pantherdb.org/

System that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in absence of direct experimental evidence. Orthologs view is curated orthology relationships between genes for human, mouse, rat, fish, worm, and fly., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PANTHER (RRID:SCR_004869) Copy   

•   Source: SciCrunch Registry

http://www.obofoundry.org/ontology/pato.html

Ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation. The new PATO differs from the old in that the system of attributes and values has been abandoned in favor of a single hierarchy of qualities. PATO is designed to be used in conjunction with ontologies of quality-bearing entities. An example of such an entity is an insect eye (taken from the fly_anatomy ontology), which could be the bearer of the quality ''red'' (PATO:0000322). This combination is the red eye phenotype. We say that the phenotype term is ''post-coordinated'', as it is formed by coordinating two terms together. This is in contrast to ontologies of pre-coordinated phenotypes, such as the Mammalian Phenotype (MP) ontology. PATO is independent of any exchange format or database schema. One way of expressing phenotype annotation using PATO is pheno-syntax, or pheno-xml. They will also post recommendations for representing phenotypes using OWL. All representations share the same basic formal underpinnings, a combination of quality-bearing entity and a quality (the EQ model).

Proper citation: PATO (RRID:SCR_004782) Copy   

•   Source: SciCrunch Registry

http://www.mercer.edu/

Private research university with its main campus in Macon, Georgia. Founded in 1833 as Mercer Institute and gaining university status in 1837.

Proper citation: Mercer University; Georgia; USA (RRID:SCR_004819) Copy   

•   Source: SciCrunch Registry

http://trackvis.org/

TrackVis is software tool that can visualize and analyze fiber track data from diffusion MR imaging (DTI/DSI/HARDI/Q-Ball) tractography. It does NOT perform actual fiber tracking. Diffusion Toolkit is a set of tools that reconstruct diffusion imaging data and generate fiber track data for TrackVis to visualize. Because these two sets of tools were developed and maintained separately and each has distinguished funtionalities, they decided to distribute them as two separate programs for the ease of maintenance and upgrade. You do need both of them to perform complete diffusion data processing and analysis. Features of TrackVis include: * Cross-platform. Works on Windows, Mac OS X and Linux with native look and feel. * A variety of track filters (track selecting methods) allowing users to explore and locate specific bundles with ease. * Multiple rendering modes with customizable scalar-driven color codes. * Real-time parameter adjustment and 3D render. * Open format of the track data file allowing users to integrate customized scalar data into the track file and visualize and analyze it. Save and restore scenes in XML style scene file. * Statistical scalar analysis of tracks and ROIs. * Synchronized real-time multiple dataset analysis and display allowing time-point and/or subject comparison. Synchronized analysis and display on same dataset can also be performed in real-time remotely over the network. * Upfront in-line parameter adjustment in real-time. No tedious pop-up dialogs. TrackVis works with Track File created by Diffusion Toolkit. Diffusion Toolkit processes raw DICOM, Nifti format and ANALYZE images. TrackVis and Diffusion Toolkit are cross-platform software. They can run on Windows XP, Mac OS X as well as Linux.

Proper citation: TrackVis (RRID:SCR_004817) Copy   

•   Source: SciCrunch Registry

http://www.ifomis.org/bfo

A small, upper level ontology that is designed for use in supporting information retrieval, analysis and integration in scientific and other domains. BFO is a genuine upper integration in scientific and other domains. Thus it does not contain physical, chemical, biological or other terms which would properly fall within the coverage domains of the special sciences.

Proper citation: BFO (RRID:SCR_004818) Copy   

•   Source: SciCrunch Registry

http://www.wallenberg.com/kaw/en

One of the largest financiers of research in Sweden that promotes scientific research, teaching and/or education beneficial to the Kingdom of Sweden. 20-30 percent of the Foundation''s grants relate to high-value research equipment for use within the technical, natural sciences and biomedical fields, and about 50 percent relate to major research projects and substantial scientific networks. Universities, academies and similar research and educational institutions are eligible for grants within the following fields: * Expensive scientific equipment * Fellowship programs initiated by the Foundation * Selected research projects of significant potential * Larger educational research projects Applications may be submitted by individual scientists, or research groups affiliated to a Swedish university or equivalent institution. An application may also be submitted by the management of a university, university college, scientific academy, or national research associations. Applications from private individuals without connection to a scientific institution are not considered.

Proper citation: Knut and Alice Wallenberg Foundation (RRID:SCR_004778) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/sagebionetworks/files/

Key Driver Analysis (KDA) is an analysis tool, as both an R package and Cytoscape plugin, for identifying key regulators of a gene regulatory network. It takes as input a gene network N (directed or undirected) and a gene set (module) G. The gene set is any subset of genes from the network N (e.g. pathway, module, ontology), permitting focus on a particular biological context. The KDA archive contains the plugin source, the plugin jar file, and several example datasets. Prerequisites: *Java, 5.0+ (www.javasoft.com) *Cytoscape, 2.6+ (www.cytoscape.org)

Proper citation: Key Driver Analysis (RRID:SCR_004899) Copy   

•   Source: SciCrunch Registry

http://compbio.cs.toronto.edu/prism/

Software for split read (reads which span across a structrual variant -- SV ) mapping and SV calling from the mapping result. It is able to detect small insertions and abitrary size deletions, inversions and tandom duplications with the direction of discordant read pairs. PRISM_CTX is a tool for detecting inter-chromosome trans-location events.

Proper citation: PRISM - Pair Read Informed Split Mapper (RRID:SCR_004812) Copy   

•   Source: SciCrunch Registry

http://ibis.tau.ac.il/miRNAkey/

A software pipeline for the analysis of microRNA Deep Sequencing data.

Proper citation: miRNAKey (RRID:SCR_004813) Copy   

•   Source: SciCrunch Registry

http://dgv.tcag.ca/dgv/app/home

Public repository that accepts direct submissions and provides archiving, accessioning and distribution of publicly available genomic structural variants, in all species. Variants are accessioned at the study and sample level, granting stable identifiers that can be used in publications. DGVa data is integrated with other EBI resources, including comprehensive EBI search and Ensembl genome browser. Exchanges data with companion database, dbVar, at National Center for Biotechnology Information.NOTE: since 2019 DGVa doesn't accept submissions. Please send the data for submission to European Variation Archive (EVA).

Proper citation: Database of Genomic Variants Archive (DGVa) (RRID:SCR_004896) Copy   

•   Source: SciCrunch Registry

http://svmerge.sourceforge.net/

Software pipeline to detect structural variants (SVs) by integrating calls from several existing SV callers, which are then validated and the breakpoints refined using local de novo assembly. The output is in BED format allowing for easy downstream analysis or viewing in a genome browser. It is modular and extensible allowing new callers to be incorporated as they become available.

Proper citation: SVMerge (RRID:SCR_004777) Copy   

•   Source: SciCrunch Registry

http://jaxmice.jax.org/strain/007910.html

These Brainbow 1.0 (founder line L) mice allow labeling of individual neuronal types (specifically hippocampal neuron cell bodies, and including motor neurons, dentate gyrus granule cells, pyramidal neurons of the cortex and CA1 area) with approximately 166 distinguishable color variations in cre recombined cells, and may also be useful in conjunction with other Brainbow strains (Stock No. 007901, Stock No. 007911, Stock No. 007921) for neurobiological studies. These Thy1-Brainbow 1.0 (line L) transgenic mice are viable and fertile. The mice possess multiple fluorescent protein sequences uniquely flanked with pairs of incompatible Lox sites alternated to create mutually exclusive recombination events; allowing stochastic expression of multiple fluorescent proteins from a single transgene. Prior to Cre-mediated recombination, the fluorescent protein immediately adjacent to the promoter, dTomato (RFP), is expressed in peripheral and central neurons. When bred to Cre recombinase expressing mice, the resulting offspring can have one of three expression outcomes for each transgene in each cell of the cre expressing tissue(s): dTomato (RFP) (no recombination), mCerulean (CFP), or mYFP. Integration of tandem transgene copies yields combinatorial fluorescent protein expression in each cell, and thus many possible cell colors, providing a way to distinguish adjacent neurons and visualize other cellular interactions. Of note, the single FRT site inserted in the transgene allows tandem transgene copy number reduction through Flp-mediated recombination if desired. These Brainbow 1.0 (founder line L) mice were found to have multiple transgene copies that allow labeling of individual neuronal types (specifically hippocampal neuron cell bodies, and including motor neurons, dentate gyrus granule cells, pyramidal neurons of the cortex and CA1 area) with approximately 166 distinguishable color variations in cre recombined cells, and may also be useful in conjunction with other Brainbow strains (Stock No. 007901, Stock No. 007911, Stock No. 007921) for neurobiological studies. This mouse can be used to support research in many areas including:
Neurobiology Research
* Cre-lox System (loxP-flanked Sequences)
* Fluorescent protein expression in neural tissue
Research Tools
* Cre-lox-System (loxP-flanked Sequences: Test/Reporter)
* Developmental Biology Research (Cre-lox system)
* Developmental Biology Research (transplantation marker for embryonic and adult tissue)
* FLP-FRT System (FRT-flanked Sequences)
* Fluorescent Proteins * Genetics Research (Mutagenesis and Transgenesis: Cre-lox system) * Genetics Research (Tissue/Cell Markers: Cre-lox system) * Genetics Research (Tissue/Cell Markers: astrocyte-specific marker) * Genetics Research (Tissue/Cell Markers: astrocytes) * Genetics Research (Tissue/Cell Markers: astrocytes, neurons) * Genetics Research (Tissue/Cell Markers: glial cells) * Genetics Research (Tissue/Cell Markers: multiple) * Genetics Research (Tissue/Cell Markers: neurons) * Genetics Research (Tissue/Cell Markers: transplantation marker for embryonic and adult tissue) * Neurobiology Research (astrocyte-specific marker) * Neurobiology Research (cell marker) * YFP related Research Tools * Fluorescent Proteins Control: 000664 C57BL/6J (approximate)

Proper citation: Brainbow mouse resource at Jackson Labs (RRID:SCR_004894) Copy   

•   Source: SciCrunch Registry

http://seqanswers.com/

An information resource and user-driven community focused on all aspects of next-generation genomics. They hope to become the central location for next generation sequencing technology discussion and education. The site will always attempt to cater to everyone, regardless of scientific background or knowledge. The High-Throughput Sequencing Map site was conceived by James Hadfield (Cancer Research UK, Cambridge) and built by Nick Loman (University of Birmingham). The database is as only as good as you, the users.

Proper citation: SEQanswers (RRID:SCR_004808) Copy   

•   Source: SciCrunch Registry

http://www.engr.uconn.edu/~jiz08001/svseq2.html

Software for accurate and efficient calling of structural variations with low-coverage sequence data. Version 2 uses the BAM files of paired Illumina reads with soft-clip signature as input. It calls both deletions and insertions.

Proper citation: SVseq (RRID:SCR_004804) Copy   

•   Source: SciCrunch Registry

http://www.science3point0.com/coaspedia/index.php/Welcome

THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 08, 2013. Wiki serving as a demo for integrating wikis with scientific workflows, extending peer review and open access from formal scholarly publishing to the whole research cycle. Just imagine you could browse science as it happens. It is intended to be launched, as a prototype, in early 2011, and any help with it is welcome just create an account and mention here how you would like to get involved. In the initial phase, the platform will primarily be used to simply archive copies of scholarly articles that were formally published under an Open license. This WikiRepository shall provide a unified front-end to search, discover and sort all these Open Access papers, and to annotate, share, bookmark and discuss them. Later on, it is intended to be complemented by a formal publishing platform, WikiJournal. From the start on, emphasis will be placed on updatability of published research, on placing new research in the context of existing knowledge as well as ongoing and even planned research on the matter, and of the communities concerned.

Proper citation: Daniel Mietchens demo wiki: What would scholarly communication look like if it were invented today? (RRID:SCR_004805) Copy   

•   Source: SciCrunch Registry

http://www.biobanks.se/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 3rd,2023. The National Biobank Program is a joint national program of two Swedish investments on functional genomics, Swegene and Wallenberg Consortium North. This web-site is intended as an information resource on biobanks in Sweden, where knowledge about the Swedish biobanking system is mediated and the progress of the National Biobanking Program is presented. You will also find a list of individual Swedish biobanks. The main objectives of the National Biobank Program are: * to increase the knowledge of the Swedish biobanking system * to increase the quality of Swedish biobanks * to increase usability and availability of samples stored in Swedish biobanks for use in research, diagnosis and treatment * to increase the safety of the providers of samples by stimulating increased protection of the personal integrity and increased ethical awareness The National Biobank Program works through financing of strategic investments to improve biobanking systems of national interest. The program has a budget of SEK 26.4 million for the period of 2002 to 2003.

Proper citation: Swedish National Biobank Program (RRID:SCR_004889) Copy   

•   Source: SciCrunch Registry

http://narc.wustl.edu/narc/default.aspx

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. The Neurologic AIDS Research Consortium (NARC) is supported by the National Institutes of Health to design and carry out clinical trials to improve the therapy for HIV induced neurologic disease, and neurologic conditions associated with the AIDS virus. This consortium was established in 1993 when the NARC grant submitted by David B. Clifford, M.D. of Washington University School of Medicine was funded by the National Institute of Neurologic Disorders and Stroke (NINDS) to establish the consortium. Since that time the grant has supported studies of the natural history of neurologic performance in advanced AIDS, treatment of HIV associated peripheral neuropathy, progressive multifocal leukoencephalopathy, and cytomegalovirus.

Proper citation: Neurologic AIDS Research Consortium (RRID:SCR_005019) Copy   

•   Source: SciCrunch Registry