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http://archive.gramene.org/plant_ontology/ontology_browse.html#eo

A structured controlled vocabulary for the representation of plant environmental conditions.

Proper citation: Plant Environmental Conditions (RRID:SCR_003460) Copy   

•   Source: SciCrunch Registry

http://ctrad-csi.nus.edu.sg/gbsa/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. Software for analyzing whole-genome bisulfite sequencing data.

Proper citation: GBSA (RRID:SCR_003413) Copy   

•   Source: SciCrunch Registry

http://www.etonbio.com/

An Antibody supplier

Proper citation: Eton Bioscience (RRID:SCR_003533) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/pride/

Centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence. Originally it was developed to provide a common data exchange format and repository to support proteomics literature publications. This remit has grown with PRIDE, with the hope that PRIDE will provide a reference set of tissue-based identifications for use by the community. The future development of PRIDE has become closely linked to HUPO PSI. PRIDE encourages and welcomes direct user submissions of protein and peptide identification data to be published in peer-reviewed publications. Users may Browse public datasets, use PRIDE BioMart for custom queries, or download the data directly from the FTP site. PRIDE has been developed through a collaboration of the EMBL-EBI, Ghent University in Belgium, and the University of Manchester.

Proper citation: Proteomics Identifications (PRIDE) (RRID:SCR_003411) Copy   

•   Source: SciCrunch Registry

http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Main_Page

Laboratory portal, including software, web-based tools, databases and data sets, related to their research that focuses on the development and application of biophysical and bioinformatics methods aimed at understanding the structural and energetic origins of protein-protein, protein-nucleic acid, and protein-membrane interactions. Their work includes fundamental theoretical research, the development of software tools, and applications to problems of biological importance. In this regard they maintain an active collaborative computational and experimental research program on the molecular basis of cell-cell adhesion. Other problems of current interest include protein structure prediction, the organization of protein sequence/structure space, the prediction of protein function based on protein structure, the structural origins of specificity in protein-DNA interactions, RNA function and, more generally, the electrostatic properties of biological macromolecules.

Proper citation: Honig Lab (RRID:SCR_003410) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/MultiPhen/

Software package that performs genetic association tests between SNPs (one-at-a-time) and multiple phenotypes (separately or in joint model).

Proper citation: MultiPhen (RRID:SCR_003498) Copy   

•   Source: SciCrunch Registry

http://www.biostat.wisc.edu/~kendzior/EBSEQ/

Software R package for RNA-Seq Differential Expression Analysis.

Proper citation: EBSeq (RRID:SCR_003526) Copy   

•   Source: SciCrunch Registry

http://en.wikibooks.org/wiki/Human_Physiology

Human Physiology is a featured book on Wikibooks because it contains substantial content, it is well-formatted, and the Wikibooks community has decided to feature it on the main page or in other places. Please continue to improve it and thanks for the great work so far! A printable and PDF version are available. You can edit its advertisement template. Contents: 1. Homeostasis 2. Cell Physiology 3. Integumentary System 4. The Nervous System 5. Senses 6. The Muscular System 7. Blood Physiology 8. The Cardiovascular System 9. The Immune System 10. The Urinary System 11. The Respiratory System 12. The Gastrointestinal System 13. Nutrition 14. The Endocrine System 15. The Male Reproductive System 16. The Female Reproductive System 17. Pregnancy and Birth 18. Genetics and Inheritance 19. Development: Birth through Death 20. Appendix 1: Answers to Review Questions 21. Authors 22. Further Reading

Proper citation: Human Physiology (RRID:SCR_003525) Copy   

•   Source: SciCrunch Registry

https://cabig.nci.nih.gov/tools/caTRIP

THIS RESOURCE IS NO LONGER IN SERVICE documented June 4, 2013. Allows users to query across a number of caBIG data services, join on common data elements (CDEs), and view results in a user-friendly interface. With an initial focus on enabling outcomes analysis, caTRIP allows clinicians to query across data from existing patients with similar characteristics to find treatments that were administered with success. In doing so, caTRIP can help inform treatment and improve patient care, as well as enable the searching of available tumor tissue, enable locating patients for clinical trials, and enable investigating the association between multiple predictors and their corresponding outcomes such as survival caTRIP relies on the vast array of open source caBIG applications, including: * Tumor Registry, a clinical system that is used to collect endpoint data * cancer Text Information Extraction System (caTIES), a locator of tissue resources that works via the extraction of clinical information from free text surgical pathology reports. while using controlled terminologies to populate caBIG-compliant data structures * caTissue CORE, a tissue bank repository tool for biospecimen inventory, tracking, and basic annotation * Cancer Annotation Engine (CAE), a system for storing and searching pathology annotations * caIntegrator, a tool for storing, querying, and analyzing translational data, including SNP data Requires Java installation and network connectivity.

Proper citation: caTRIP (RRID:SCR_003409) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/pharmgkb-owl/

An OWL representation of the data in PharmGKB, Comparative Toxicogenomics Database (CTD) and DrugBank and linked to related ontologies: ChEBI ontology, the Human Disease Ontology (DO), the Anatomical Therapeutic Chemical Classification System (ATC) and the Medical Subject Headings Thesaurus (MESH). The combined knowledge base can be exploited using the ELK reasoner.

Proper citation: PharmGKB Ontology (RRID:SCR_003529) Copy   

•   Source: SciCrunch Registry

http://www.reactome.org

Collection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets.

Proper citation: Reactome (RRID:SCR_003485) Copy   

•   Source: SciCrunch Registry

http://www.hsph.harvard.edu/skat/metaskat/

A R package for multiple marker meta-analysis.

Proper citation: MetaSKAT (RRID:SCR_003489) Copy   

•   Source: SciCrunch Registry

http://genomesavant.com/p/home/index

Next-generation genome browser software designed for the latest generation of genome data.

Proper citation: Savant (RRID:SCR_003488) Copy   

•   Source: SciCrunch Registry

http://mimi.ncibi.org/MimiWeb/main-page.jsp

MiMi Web gives you an easy to use interface to a rich NCIBI data repository for conducting your systems biology analyses. This repository includes the MiMI database, PubMed resources updated nightly, and text mined from biomedical research literature. The MiMI database comprehensively includes protein interaction information that has been integrated and merged from diverse protein interaction databases and other biological sources. With MiMI, you get one point of entry for querying, exploring, and analyzing all these data. MiMI provides access to the knowledge and data merged and integrated from numerous protein interactions databases and augments this information from many other biological sources. MiMI merges data from these sources with deep integration into its single database with one point of entry for querying, exploring, and analyzing all these data. MiMI allows you to query all data, whether corroborative or contradictory, and specify which sources to utilize. MiMI displays results of your queries in easy-to-browse interfaces and provides you with workspaces to explore and analyze the results. Among these workspaces is an interactive network of protein-protein interactions displayed in Cytoscape and accessed through MiMI via a MiMI Cytoscape plug-in. MiMI gives you access to more information than you can get from any one protein interaction source such as: * Vetted data on genes, attributes, interactions, literature citations, compounds, and annotated text extracts through natural language processing (NLP) * Linkouts to integrated NCIBI tools to: analyze overrepresented MeSH terms for genes of interest, read additional NLP-mined text passages, and explore interactive graphics of networks of interactions * Linkouts to PubMed and NCIBI's MiSearch interface to PubMed for better relevance rankings * Querying by keywords, genes, lists or interactions * Provenance tracking * Quick views of missing information across databases. Data Sources include: BIND, BioGRID, CCSB at Harvard, cPath, DIP, GO (Gene Ontology), HPRD, IntAct, InterPro, IPI, KEGG, Max Delbreuck Center, MiBLAST, NCBI Gene, Organelle DB, OrthoMCL DB, PFam, ProtoNet, PubMed, PubMed NLP Mining, Reactome, MINT, and Finley Lab. The data integration service is supplied under the conditions of the original data sources and the specific terms of use for MiMI. Access to this website is provided free of charge. The MiMI data is queryable through a web services api. The MiMI data is available in PSI-MITAB Format. These files represent a subset of the data available in MiMI. Only UniProt and RefSeq identifiers are included for each interactor, pathways and metabolomics data is not included, and provenance is not included for each interaction. If you need access to the full MiMI dataset please send an email to mimi-help (at) umich.edu.

Proper citation: Michigan Molecular Interactions (RRID:SCR_003521) Copy   

•   Source: SciCrunch Registry

http://cng.gmu.edu:8080/Lm

A freely available software tool available for the Windows and Linux platform, as well as the Online version Applet, for the analysis, comparison and search of digital reconstructions of neuronal morphologies. For the quantitative characterization of neuronal morphology, LM computes a large number of neuroanatomical parameters from 3D digital reconstruction files starting from and combining a set of core metrics. After more than six years of development and use in the neuroscience community, LM enables the execution of commonly adopted analyses as well as of more advanced functions, including: (i) extraction of basic morphological parameters, (ii) computation of frequency distributions, (iii) measurements from user-specified subregions of the neuronal arbors, (iv) statistical comparison between two groups of cells and (v) filtered selections and searches from collections of neurons based on any Boolean combination of the available morphometric measures. These functionalities are easily accessed and deployed through a user-friendly graphical interface and typically execute within few minutes on a set of 20 neurons. The tool is available for either online use on any Java-enabled browser and platform or may be downloaded for local execution under Windows and Linux.

Proper citation: L-Measure (RRID:SCR_003487) Copy   

•   Source: SciCrunch Registry

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

A Java interface to the mzTab data exchange format for reporting a summary of proteomics results.

Proper citation: jmzTab (RRID:SCR_003481) Copy   

•   Source: SciCrunch Registry

http://images.nigms.nih.gov/

Database of scientific photos, illustrations, and videos made available by the National Institute of General Medical Sciences.

Proper citation: National Institute of General Medical Sciences Image Gallery (RRID:SCR_003480) Copy   

•   Source: SciCrunch Registry

http://www.idoimaging.com/program/280

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023.Comprised of a large array of sophisticated programs, this comprehensive software package with tools based around the MINC file format. Utilities are provided for conversion, viewing, editing, registering, segmentation, and a wide array of analysis. Many programs are in Perl. MINC software tools for neurological imaging are free. Input format: Analyze, DICOM, Minc

Proper citation: MINC Brain Imaging Toolbox (RRID:SCR_003519) Copy   

•   Source: SciCrunch Registry

http://www.wikisurgery.com/index.php?title=Main_Page

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. A free surgical encyclopedia for surgeons and their patients. Contributions in the form of new articles and editing can be made by anyone at anytime anywhere in the world. With over 33,000 articles for surgeons and patients, including news, articles, operation scripts, biographies and images. The website is a "wiki" which allows for the collaborative editing and building of content. Contributions in the form of new articles and editing can be made by those who register on the site, confirm their email address and whose application is accepted by an administrator. Wikisurgery is more than just a depot of surgical knowledge, not just articles about facts but also articles about controversy, debates, with none of the usual editorial limits on space. Indeed we hope it will become a record of surgical thought, experience and progression. Key Topics: Operation Scripts, Basic Surgical Skills Training Program, Basic Laparoscopic Training Program, Operative Images, Patient Information; there is also a Featured Videos section.

Proper citation: WikiSurgery - The Free Surgical Encyclopedia (RRID:SCR_003556) Copy   

•   Source: SciCrunch Registry

http://www.oae-ontology.org

Biomedical ontology in the domain of adverse events that aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. AEO is a community-based ontology. Its development follows the OBO Foundry principles.

Proper citation: Ontology of Adverse Events (RRID:SCR_003428) Copy   

•   Source: SciCrunch Registry