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http://metaphyler.cbcb.umd.edu/

A taxonomic classifier for metagenomic shotgun reads, which uses phylogenetic marker genes as a taxonomic reference. The classifier, based on BLAST, uses different thresholds (automatically learned from the reference database) for each combination of taxonomic rank, reference gene, and sequence length. The reference database includes marker genes from all complete genomes, several draft genomes and the NCBI nr protein database.

Proper citation: MetaPhyler (RRID:SCR_004848) Copy   

•   Source: SciCrunch Registry

https://www.fieldtriptoolbox.org

Software toolbox for analysis of MEG, EEG, and other electrophysiological data. Used by experimental neuroscientists.

Proper citation: FieldTrip (RRID:SCR_004849) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.fh-stralsund.de/nucpos/

A simulation tool to identify positions of nucleosomes from Next Generation Sequencing data.

Proper citation: NucPosSimulator (RRID:SCR_004765) Copy   

•   Source: SciCrunch Registry

http://huttenhower.sph.harvard.edu/metaphlan2

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. It relies on unique clade-specific marker genes identified from reference genomes.

Proper citation: MetaPhlAn (RRID:SCR_004915) Copy   

•   Source: SciCrunch Registry

http://scicrunch.org

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 26, 2019.An international Non-Profit Organization that advocates Open Access for never-before-published research papers on the web and provides Self-Archiving platform to enable better knowledge sharing in a way that''s easy to publish. They collect scientific material (not only publications), e.g., Journal Articles, Theses or Dissertations, Departmental Bulletin Papers, Conference Papers, Presentations, Books, Technical Reports, Research Papers, Articles, Preprints, Learning Materials, Others. If you have such a paper and would like to add a Creative Commons license to your work, or if your working organization has no Institutional Repository (IR), Open your archives to spread them to the world. How to use: 1. Sign in with Twitter 2. Select PDF and add a Creative Commons license 3. Publish and Share on Social Media Video tutorial: http://myopenarchive.org/whatsmyoa

Proper citation: MyOpenArchive (RRID:SCR_004917) Copy   

•   Source: SciCrunch Registry

http://u-compare.org/

An integrated text mining / natural language processing system based on the Unstructured Information Management Architecture (UIMA) Framework. It allows interoperability of text mining tools and allows the creation of text mining workflows, comparison and visualization of tools. U-Compare can be launched straight from the web or downloaded. As the name implies comparison of components and workflows is a central feature of the system. U-Compare allows sets of components to be run in parallel on the same inputs and then automatically generates statistics for all possible combinations of these components. Once a workflow has been created in U-Compare it can be exported and shared with other users or used with other UIMA compatible tools and so in addition to comparison, U-Compare also functions as a general purpose workflow creation tool. It contains a repository of 50+ biomedical text mining components. These components are included in the U-Compare single-click-to-launch package, ready to use by just drag-and-drop. You can also use this repository independent from the U-Compare system. Link with Taverna It has a link with Taverna for scientific workflows, http://bioinformatics.oxfordjournals.org/content/26/19/2486.abstract, where you can use U-Compare and its workflow from within the Taverna workflow. There are two ways, the U-Compare Taverna plugin and the U-Compare command line mode as a Taverna activity. We have recently integrated it with Peter Murray-Rust''''s OSCAR for Chemistry (see http://www.nactem.ac.uk/cheta/) Web Demo: http://www.nactem.ac.uk/software/cheta/

Proper citation: U-Compare (RRID:SCR_004911) Copy   

•   Source: SciCrunch Registry

http://www.capitalbiosciences.com/

Biological products including Cell Immortalization Products, Clinically Defined Human Tissue, cDNA ORF Clones, Premade Adenoviruses, Purified Proteins, Viral Expression Systems and others as well as services like Custom Recombinant Adenovirus Production, Custom Recombinant Lentivirus Production, Protein Detection and Quantification and Stable Cell Line Production for academic and governmental research institutes, pharmaceutical and biotechnology industry. Capital Biosciences offers most types of human tissues, normal and diseased, with extensive clinical history and follow up information. Standard specimen format: Snap-frozen(flash-frozen), Formalin fixed and paraffin embedded (FFPE) tissues, Blood and blood products, Bone marrow, Total RNA, Genomic DNA, Total Proteins, Primary cell cultures, Viable frozen tissue. Tumor tissue samples include: Bladder cancer, Glioblastoma, Medulloblastoma, Breast Carcinoma, Cervical Cancer, Colorectal Cancer, Endometrial Cancer, Esophageal Cancer, Head and Neck (H&N) Carcinoma, Hepatocellular Carcinoma (HCC), Hodgkin's lymphoma, Kidney, Renal Cell Carcinoma, Lung Cancer, Non-Small Cell (NCSLC), Lung Cancer, Small Cell (SCLC), Melanoma, Mesothelioma, non-Hodgkin's Lymphoma, Ovarian Adenocarcinoma, Pancreatic Cancer, Prostate Cancer, Stomach Cancer.

Proper citation: Capital Biosciences (RRID:SCR_004879) Copy   

•   Source: SciCrunch Registry

http://useq.sourceforge.net/

A collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms.

Proper citation: USeq (RRID:SCR_004753) Copy   

•   Source: SciCrunch Registry

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