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http://www.ncbi.nlm.nih.gov/biosystems/

Database that provides access to biological systems and their component genes, proteins, and small molecules, as well as literature describing those biosystems and other related data throughout Entrez. A biosystem, or biological system, is a group of molecules that interact directly or indirectly, where the grouping is relevant to the characterization of living matter. BioSystem records list and categorize components, such as the genes, proteins, and small molecules involved in a biological system. The companion FLink tool, in turn, allows you to input a list of proteins, genes, or small molecules and retrieve a ranked list of biosystems. A number of databases provide diagrams showing the components and products of biological pathways along with corresponding annotations and links to literature. This database was developed as a complementary project to (1) serve as a centralized repository of data; (2) connect the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system; and (3) facilitate computation on biosystems data. The NCBI BioSystems Database currently contains records from several source databases: KEGG, BioCyc (including its Tier 1 EcoCyc and MetaCyc databases, and its Tier 2 databases), Reactome, the National Cancer Institute's Pathway Interaction Database, WikiPathways, and Gene Ontology (GO). It includes several types of records such as pathways, structural complexes, and functional sets, and is desiged to accomodate other record types, such as diseases, as data become available. Through these collaborations, the BioSystems database facilitates access to, and provides the ability to compute on, a wide range of biosystems data. If you are interested in depositing data into the BioSystems database, please contact them.

Proper citation: NCBI BioSystems Database (RRID:SCR_004690) Copy   

•   Source: SciCrunch Registry

http://www.nlmsf.org/

A volunteer, not for profit organization providing leadership in supporting research of LeioMyoSarcoma, improving treatment outcomes of those affected by this disease as well as fostering awareness in the medical community and general public. All dollars go to research and awareness. Leiomyosarcoma is a rare form of cancer, which affects about four people in every million. It spreads through the blood stream and can affect the lungs, liver, blood vessels or any other soft tissue in the body. Presently there is no cure, only remission if it can be attained, and this rare cancer can reappear anywhere and at any time. Because of its rarity, few doctors know how to treat it and it attracts little research. The National LeioMyoSarcoma Foundation hosts several Fundraising events throughout the year.

Proper citation: National LeioMyoSarcoma Foundation (RRID:SCR_004692) Copy   

•   Source: SciCrunch Registry

http://www.ganfyd.org/index.php?title=Main_Page

Simply put ganfyd is an evolving textbook of medicine: a free medical knowledge base that anyone can read and any registered medical practitioner may edit. This collaborative medical reference by medical professionals and invited non-medical experts is based around the wiki format, enabling true sharing of knowledge. Please join and help us to create a great source of information and experience! Ganfyd is the first of its type and relies on your contributions to make it a truly world-class resource. Contents: * Medical Specialties * Surgical Specialties * Primary Care * Public Health * Laboratory-based specialties * Imaging Specialties * Basic Medical Sciences * Miscellaneous * Women''s health * Survival Guides * How-tos & Practical Advice * Resources for Trainees * Computing * Medical Dictionary

Proper citation: Ganfyd - Get A Note From Your Doctor (RRID:SCR_004606) Copy   

•   Source: SciCrunch Registry

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

Non-profit academic organization for research and services in bioinformatics. Provides freely available data from life science experiments, performs basic research in computational biology, and offers user training programme, manages databases of biological data including nucleic acid, protein sequences, and macromolecular structures. Part of EMBL.

Proper citation: European Bioinformatics Institute (RRID:SCR_004727) Copy   

•   Source: SciCrunch Registry

http://www.journalguide.com

Database of journal information that provides tools to search, sort, filter, compare, and evaluate scholarly journals. In addition to searching by journal name, category or publisher, authors can use title and abstract of paper to discover journals that have already published articles on similar topics. Data sources include major industry data sets, public resources, information submitted directly by journal editors, and real-life publishing experiences submitted by authors.

Proper citation: JournalGuide (RRID:SCR_003236) Copy   

•   Source: SciCrunch Registry

http://www.openscholarship.org/jcms/c_5012/en/

An organization for universities and research institutions that is an information service and a forum for raising and discussing issues around the mission of modern universities and research institutions, particularly with regard to the creation, dissemination and preservation of research findings. Its aim is to further the opening up of scholarship and research that we are now seeing through the growing open access, open education, open science and open innovation movements. These, and other, "open" approaches to scholarship are changing the way research and learning are done and there are profound implications for universities and research institutions. EOS has been established to help guide developments and to assist others in understanding the issues and their implications. The context in which EOS has been established is that of increasing interest from governments, funders and the research community itself in opening up the way research is carried out and communicated. This interest is complemented by new research practices and processes that can work effectively only in an open, collaborative environment. Developments of relevance to the mission of EnablingOpenScholarship are reported on and news and details of forthcoming meetings, briefings and discussion sessions is provided.

Proper citation: EnablingOpenScholarship (RRID:SCR_003235) Copy   

•   Source: SciCrunch Registry

http://citationstyles.org/

An open XML-based language used to describe the formatting of citations and bibliographies. CSL has become the standard way to add citation support to software.

Proper citation: Citation Style Language (RRID:SCR_003234) Copy   

•   Source: SciCrunch Registry

http://function.princeton.edu/GOLEM/index.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented July 7, 2017. Welcome to the home of GOLEM: An interactive, graphical gene-ontology visualization, navigation,and analysis tool on the web. GOLEM is a useful tool which allows the viewer to navigate and explore a local portion of the Gene Ontology (GO) hierarchy. Users can also load annotations for various organisms into the ontology in order to search for particular genes, or to limit the display to show only GO terms relevant to a particular organism, or to quickly search for GO terms enriched in a set of query genes. GOLEM is implemented in Java, and is available both for use on the web as an applet, and for download as a JAR package. A brief tutorial on how to use GOLEM is available both online and in the instructions included in the program. We also have a list of links to libraries used to make GOLEM, as well as the various organizations that curate organism annotations to the ontology. GOLEM is available as a .jar package and a macintosh .app for use on- or off- line as a stand-alone package. You will need to have Java (v.1.5 or greater) installed on your system to run GOLEM. Source code (including Eclipse project files) are also available. GOLEM (Gene Ontology Local Exploration Map)is a visualization and analysis tool for focused exploration of the gene ontology graph. GOLEM allows the user to dynamically expand and focus the local graph structure of the gene ontology hierarchy in the neighborhood of any chosen term. It also supports rapid analysis of an input list of genes to find enriched gene ontology terms. The GOLEM application permits the user either to utilize local gene ontology and annotations files in the absence of an Internet connection, or to access the most recent ontology and annotation information from the gene ontology webpage. GOLEM supports global and organism-specific searches by gene ontology term name, gene ontology id and gene name. CONCLUSION: GOLEM is a useful software tool for biologists interested in visualizing the local directed acyclic graph structure of the gene ontology hierarchy and searching for gene ontology terms enriched in genes of interest. It is freely available both as an application and as an applet.

Proper citation: GOLEM An interactive, graphical gene-ontology visualization, navigation, and analysis tool (RRID:SCR_003191) Copy   

•   Source: SciCrunch Registry

http://www.vision.edu.au/

Centre of Excellence in Vision Science that brings together major vision research programs at the The Australian National University with cognate programs at the Universities of Queensland, Sydney and Western Australia. The research is focused on unravelling the cellular basis of visual sensing and processing; on revealing the algorithms that underlie the visual control of behavior and perception; and on discovering the cellular mechanisms that make the eye and retina stable, and whose breakdown causes blindness.

Proper citation: ARC Centre of Excellence in Vision Science (RRID:SCR_003196) Copy   

•   Source: SciCrunch Registry

http://www.icpsr.umich.edu/

Data archive of more than 500,000 files of research in the social sciences, hosting 16 specialized collections of data in education, aging, criminal justice, substance abuse, terrorism, and other fields. ICPSR comprises a consortium of about 700 academic institutions and research organizations providing training in data access, curation, and methods of analysis for the social science research community. ICPSR welcomes and encourages deposits of digital data. ICPSR's educational activities include the Summer Program in Quantitative Methods of Social Research external link, a comprehensive curriculum of intensive courses in research design, statistics, data analysis, and social methodology. ICPSR also leads several initiatives that encourage use of data in teaching, particularly for undergraduate instruction. ICPSR-sponsored research focuses on the emerging challenges of digital curation and data science. ICPSR researchers also examine substantive issues related to our collections, with an emphasis on historical demography and the environment.

Proper citation: Inter-university Consortium for Political and Social Research (ICPSR) (RRID:SCR_003194) Copy   

•   Source: SciCrunch Registry

http://www.wikispaces.com/

A social writing platform, free for education, to easily create a classroom workspace where teacher and students can communicate and work on writing projects alone or in teams. Rich assessment tools give the power to measure student contribution and engagement in real-time. Wikispaces Classroom works great on modern browsers, tablets, and phones. For a fee it is also available to non-educators including companies, organizations, universities, groups, etc.

Proper citation: Wikispaces (RRID:SCR_003228) Copy   

•   Source: SciCrunch Registry

http://wiki.solariseclipse.net/PrimerDesigner

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Software program to aid in designing of primers and creation of primer sheets. The program allows users to select a background and enter mutaions. An initial primer is then suggested. User can manipulate the selected primer to add or remove nucleotides from either 5? or 3? ends. A set of parameters reflecting the goodness of the primer is updated on the fly, as the user makes changes. Once happy with the primer, the information is saved in a primer sheet, which can then be uploaded to the BGME lab primer database on the Wiki.

Proper citation: Primer Designer (RRID:SCR_003189) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/salt1/

Software that can accurately and sensitivity classify short reads of next-generation sequencing (NGS) into protein domain families. It is based on profile HMM and a supervised graph contribution algorithm. Compared to existing tools, it has high sensitivity and specificity in classifying short reads into their native domain families.

Proper citation: SALT (RRID:SCR_003187) Copy   

•   Source: SciCrunch Registry

http://resexomedb.bioinf-dz.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. An online catalog for whole-exome sequencing (WES) results including mutations and gene-disease associations identified by WES. It is browsable and searchable by mutation, gene, study or publication. In addition, it centralizes all publications, software, platforms related to exome / whole genome sequencing.

Proper citation: resExomeDB (RRID:SCR_003224) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/xorro-overlap/

Efficient paired-read overlap software program for use with Illumina sequencing.

Proper citation: XORRO (RRID:SCR_003181) Copy   

•   Source: SciCrunch Registry

http://www.gimp.org

A software application for such tasks as photo retouching, image composition and image authoring. It has many capabilities such as it can be used as a simple paint program, an expert quality photo retouching program, an online batch processing system, a mass production image renderer, an image format converter, etc. GIMP is expandable and extensible and designed to be augmented with plug-ins and extensions. The advanced scripting interface allows everything from the simplest task to the most complex image manipulation procedures to be easily scripted.

Proper citation: GNU Image Manipulation Program (RRID:SCR_003182) Copy   

•   Source: SciCrunch Registry

https://rostlab.org/owiki/index.php/PredictNLS

Software automated tool for analysis and determination of Nuclear Localization Signals (NLS). Predicts that your protein is nuclear or finds out whether your potential NLS is found in our database. The program also compiles statistics on the number of nuclear/non-nuclear proteins in which your potential NLS is found. Finally, proteins with similar NLS motifs are reported, and the experimental paper describing the particular NLS are given.

Proper citation: PredictNLS (RRID:SCR_003133) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/APO

A structured controlled vocabulary for the phenotypes of Ascomycete fungi.

Proper citation: Ascomycete Phenotype Ontology (RRID:SCR_003254) Copy   

•   Source: SciCrunch Registry

http://www.crdamc.amedd.army.mil/behav-health/strong-star.aspx

A multidisciplinary and multi-institutional research consortium to develop and evaluate the most effective early interventions possible for the detection, prevention, and treatment of combatrelated posttraumatic stress disorder (PTSD) in activeduty military personnel and recently discharged veterans. Complementary investigations are focused on the root causes of PTSD, including biological factors that influence PTSD susceptibility and recovery; the influence of comorbid physical and psychological ailments; and the interaction of cognitive-behavioral therapies and pharmacologic treatments. The full cohort of STRONG STAR trials include: Treatment Studies, Biological Studies, Epidemiological Studies, and Preclinical Studies. STRONG STAR is currently conducting three clinical treatment trials at Carl R. Darnall Army Medical Center (CRDAMC). The studies are examining the effectiveness of Cognitive Processing Therapy (CPT), Prolonged Exposure Therapy (PE) and Cognitive Behavioral Therapy for Insomnia (CBTi) with active duty service members. Treatments are offered in individual, group, and online formats, and last from two to eight weeks. Study participants must be active duty service members who will remain in the Ft Hood area for at least 34 months to complete initial assessments and treatment programs. Referrals to the treatment studies can be made through a behavioral health provider or through selfreferral., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Strong Star (RRID:SCR_003132) Copy   

•   Source: SciCrunch Registry

https://github.com/arq5x/lumpy-sv/

Software package as probabilistic framework for structural variant discovery. Capable of integrating any number of SV detection signals including those generated from read alignments or prior evidence. Simplified wrapper for standard analyses, LUMPY Express, can also be executed.

Proper citation: LUMPY (RRID:SCR_003253) Copy   

•   Source: SciCrunch Registry