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http://iubio.bio.indiana.edu/webapps/SeWeR/

Sequence analysis using Web Resources (SeWeR) is an integrated, Dynamic HTML (DHTML) interface to commonly used bioinformatics services available on the World Wide Web. It is highly customizable, extendable, platform neutral, completely server-independent and can be hosted as a web page as well as being used as stand-alone software running within a web browser. It doesn''t require any server to host itself. The goal of SeWeR is to turn your web-browser into a powerful sequence-analysis tool. It is written entirely in JavaScript1.2. SeWeR can be downloaded and mirrored freely. The whole package is just around 300K. You can even run it from a floppy. SeWeR is not compatible with Netscape 6. SeWeR now generates graphics. Savvy is a plasmid drawing software that generates plasmid map in the revolutionary Scalable Vector Graphics format from W3C.

Proper citation: SeWeR - SEquence analysis using WEb Resources (RRID:SCR_004167) Copy   

•   Source: SciCrunch Registry

http://www.smbs.buffalo.edu/pmy/

The Department of Pharmacology and Toxicology strives to maintain excellence in the areas of research, teaching and service to the School, University, and Community. The Department offers a program of didactic course work and research training leading to the degree of Doctor of Philosophy in Pharmacology, either through the Interdisciplinary Graduate Program in Biomedical Sciences (IGPBS) or through the Medical Scientist Training Program (MSTP). Pharmacology and Toxicology have similar basic principles and often utilize similar experimental methods and approaches to address a wide range of biomedical and health-related questions. Both are sciences that are basic not only to medicine, but also to pharmacy, nursing, dentistry, public health, and veterinary medicine. Additional programs are offered for the Bachelor of Science, or a combined Bachelor of Science / Master of Science in Pharmacology and Toxicology, and a Master of Arts in Pharmacology. The graduate programs are structured to provide the candidate with a broad training in basic areas of pharmacology as well as a degree of expertise in one research area including: Neuropharmacology, Psychopharmacology, Toxicology, Molecular and Cellular Pharmacology, Clinical Pharmacology

Proper citation: University at Buffalo SMBS Department of Pharmacology and Toxicology (RRID:SCR_004204) Copy   

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http://wikikidney.org/index.php/Main_Page

Wikikidney.org is an effort to prevent kidney diseases and achieve better outcomes in those who have end stage renal disease. Our mission is to use this medium to make the public more aware of kidney disease in a sincere effort to prevent it when we can, and to help our colleagues achieve good outcomes in those who already have end stage renal disease. Our role is to provide as much information as possible to patients, professionals and the general public, with the hopes that this education will be a motivating factor in making the necessary changes to prevent or stall chronic kidney disease. After nearly two decades of seeing patients with end stage renal disease, it is apparent that much of what we deal with can be delayed or prevented altogether. Several medical trials and innovations in the last several years have confirmed these observations, and form the basis of this website. A major element in preventing renal illness is simply early detection, and for this one needs education. As the Internet expands and becomes more and more a tool of everyday life, we will have the ability to access and distribute information like no other generation before us. Qualified readers are encouraged to contribute to existing articles and to create articles of their own. Contents * 1 Kidney Resources - NIC * 2 Especially for Patients * 3 General Kidney Resources * 4 Issues in Nephrology * 5 Clinical Wiki Projects * 6 Be an author, editor or reviewer on wikikidney * 7 Clinical Trials * 8 Newsdesk Top Stories * 9 Essential Physician Resources * 10 Organizations * 11 Government Agencies * 12 Vendor and other Sites * 13 Patents * 14 Index

Proper citation: Wikikidney.org (RRID:SCR_004288) Copy   

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http://brainarchitecture.org/

Evolving portal that will provide interactive tools and resources to allow researchers, clinicians, and students to discover, analyze, and visualize what is known about the brain's organization, and what the evidence is for that knowledge. This project has a current experimental focus: creating the first brainwide mesoscopic connectivity diagram in the mouse. Related efforts for the human brain currently focus on literature mining and an Online Brain Atlas Reconciliation Tool. The primary goal of the Brain Architecture Project is to assemble available knowledge about the structure of the nervous system, with an ultimate emphasis on the human CNS. Such information is currently scattered in research articles, textbooks, electronic databases and datasets, and even as samples on laboratory shelves. Pooling the knowledge across these heterogeneous materials - even simply getting to know what we know - is a complex challenge that requires an interdisciplinary approach and the contributions and support of the greater community. Their approach can be divided into 4 major thrusts: * Literature Curation and Text Mining * Computational Analysis * Resource Development * Experimental Efforts

Proper citation: Brain Architecture Project (RRID:SCR_004283) Copy   

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http://www.obofoundry.org/ro/

The OBO Relation Ontology is an ontology of core relations for use by OBO Foundry ontologies. To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena. The OBO Relation ontology is undergoing substantial changes: * Core domain-independent relations will live in BFO * Biology specific relations (defined in terms of core relations) will live in RO

Proper citation: OBO Relation Ontology (RRID:SCR_004285) Copy   

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http://www.uniprot.org/keywords/

UniProtKB entries are tagged with keywords that can be used to retrieve particular subsets of entries. There are 10 categories of keywords: Biological process Cellular component Coding sequence diversity Developmental stage Disease Domain Ligand Molecular function Post-translation modification Technical term You may browse by hierarchy, search in Keywords, or list all keywords. By default, searching the keywords will look for matches in both name and definition.

Proper citation: UniProtKB Keywords (RRID:SCR_004313) Copy   

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http://magnet.c2b2.columbia.edu/

The mission of the Center for the Multiscale Analysis of Genomic and Cellular Networks (MAGNet) is to develop novel Structural and Systems Biology methods and tools for the dissection of molecular interactions in the cell and for the interaction-based elucidation of cellular phenotypes. These tools are made freely available to the the members of the research community. They are also validated in the context of the Center''''s own research program through collaborative projects with experimental biologists. MAGNet is one of 7 National Centers for Biomedical Computing (NCBC). These Centers, in conjunction with individual investigator awards, are creating a networked effort to build the computational infrastructure for biomedical computing in the nation. The NCBC program is devoted to all facets of biomedical computing, from basic research in computational science to providing the tools and resources that biomedical and behavioral researchers need to do their work. In addition to carrying out fundamental research the NCBCs play a major role in educating and training researchers to engage in biomedical computing. MAGNet is also one of 12 inter-disciplinary Centers for Cancer Systems Biology (CCSBs), a component of the National Cancer Institute''''s Integrative Cancer Biology Program. The CCSBs provide a core framework for applying systems biology approaches to cancer research through the development and implementation of computational models of processes relevant to cancer prevention, diagnostics and therapeutics. The CCSBs seek to integrate experimental biology with mathematical modeling to foster new insights in the biology and new approaches to the management of cancer. MAGNet''''s Training Core ensures that the methods developed by the Center are integrated into the educational offerings of Columbia University''''s Medical School.

Proper citation: MAGNet - Multiscale Analysis of Genomic and Cellular Networks (RRID:SCR_004399) Copy   

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http://okcam.cbi.pku.edu.cn/ontology.php

CAMO (Cell Adhesion Molecule Ontology) is a set of standard vocabulary that provide a hierarchical description of cell adhesion molecules and their functions. We compiled a list for cell adhesion molecules by integrating Gene Ontology annotations, domain structure information, and keywords query against NCBI Entrez Gene annotations. Totally 496 unique human genes were identified to function as cell adhesion molecules, which is by far the most comprehensive dataset including cadherin, immunoglobulin/FNIII, integrin, neurexin, neuroligan, and catenin families. CAMO was constructed as a directed acyclic graph (DAG) using DAG-Edit to input, manage and update data. We annotated each term with name, definition and source references, as well as the relationship to other terms, based on manual reviews of domain architecture and functional annotations. If vertices represent terms and the relationships between terms are represented by edges, the terms in a DAG can be connected via a directed graph without cycles. CAMO thus provides a hierarchical description of functions of CAMs with five top-level categories: CAM gene families, CAM genetics, CAM regulation, CAM expression and CAM diseases. Each top-level term is further divided into several categories to describe the functions in detail.

Proper citation: CAMO - Cell Adhesion Molecule Ontology (RRID:SCR_004392) Copy   

•   Source: SciCrunch Registry

http://www.uca.edu.ar/index.php/home/index/en/universidad/facultades/buenos-aires/cs-medicas/investigacion/iib/

The Biomedical Research Program (PIB) of the School of Medical Sciences was created in 2007, after a Collaboration Protocol was established between UCA and the National Council of Scientific and Technical Research (CONICET). Research at PIB aims at unraveling the molecular, biochemical and genetic aspects of human diseases, therefore contributing to understanding complex pathologies. Research Groups include: * Molecular and Cell Biology Lab (LBCM) - Group leader: Tom��s A. Santa Coloma, Ph.D. * Nanotechnology Lab - Group leader: Tom��s A. Santa Coloma, Ph.D. * Molecular Neurobiology Lab - Group leader: Francisco J. Barrantes, Ph.D.

Proper citation: Biomedical Research Program UCA (RRID:SCR_004395) Copy   

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http://taylorlab.ucsf.edu/software_data.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documentedt on January 10, 2023. Software that implements babel routines for identifying unusual ribosome protected fragment counts given mRNA counts, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Babel (RRID:SCR_004307) Copy   

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http://www.egappreviews.org/

Initiative to develop a systematic, evidence-based process for evaluating genetic tests and other applications of genomic technology that are rapidly moving from research to use in clinical practice. A key objective of this process is to provide objective, timely, and credible information that is clearly linked to the scientific evidence on specific applications of genetic and genomic tests. The primary focus of EGAPP activities is an independent, nonfederal expert panel, the EGAPP Working Group. Other components of the EGAPP initiative include a federal interagency, the CDC staff and consultants, and an EGAPP initiative evaluation team.

Proper citation: EGAPP (RRID:SCR_004189) Copy   

•   Source: SciCrunch Registry

http://www.braintumourbank.ca/pages/about.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. The mission of the Canadian Virtual Brain Tumour Bank (CVBTB) is to facilitate clinical, molecular and translational research through the provision of well-characterized tissue linked to clinical data and to become a standardized national tissue resource whereby scientific needs are met, addressed and accelerated through a common public accessible core the CVBTB. Recognizing the need to encourage systemic banking of brain tumor tissues throughout the country and to link banks of brain tumor tissue samples with academic and scientific institutions that require these samples, the CVBTB was established. Under the sponsorship of Schering Plough Canada Inc. and in association with the Canadian Brain Tumour Consortium (CBTC), the CVBTB looks to act as a resource for all researchers to provide them with information on the types of brain tumor tissue samples available and to direct them to the tumor tissue banking sites holding these samples. The CVBTB also looks to provide information on standard operating procedures regarding aspects of tumor tissue banking such as tissue accrual, storage and shipment and the processing of blood samples such as serum and lymphocytes. The CVBTB currently consists of four brain tumour tissue banking sites (Toronto Western Hospital - Toronto, Ontario; London Health Sciences Centre - London, Ontario; McGill University - Montreal, Quebec; University of Calgary - Calgary, Alberta) and is continuously looking for more institutions to be a part of the CVBTB. If your institution would like to become a part of the CVBTB, please contact the CVBTB coordinator.

Proper citation: Canadian Virtual Brain Tumour Bank (RRID:SCR_004221) Copy   

•   Source: SciCrunch Registry

http://SchistoDB.net

SchistoDB is a genomic database for the parasitic organism Schistosoma mansoni, one of the major causative agents of schistosomiasis worldwide. It currently incorporates sequences and annotation for S. mansoni in a single user-friendly database. Several genomic scale analyses are available as well as ESTs, oligonucleotides, metabolic pathways and drugs. Make your data available: If you''d like to have your updates and/or datasets integrated in SchistoDB, drop us an email.

Proper citation: Schistosoma mansoni Database (RRID:SCR_004341) Copy   

•   Source: SciCrunch Registry

http://images.wellcome.ac.uk/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023.Digital collection of images, with themes ranging from medical and social history to contemporary healthcare and biomedical science. The collection contains historical images from the Wellcome Library collections, Tibetan Buddhist paintings, ancient Sanskrit manuscripts written on palm leaves, beautifully illuminated Persian books and much more. The Biomedical Collection holds over 40 000 high-quality images from the clinical and biomedical sciences. Selected from the UK''s leading teaching hospitals and research institutions, it covers disease, surgery, general healthcare, sciences from genetics to neuroscience including the full range of imaging techniques. They are always looking for new high quality biomedical images from scientific researchers, clinical photographers and artists in any field of science or medicine. As a contributor you retain your original material and copyright, and receive commission and full credit each time your images are used. The annual Wellcome Images awards (previously known as Biomedical Images Awards) reward contributors for their outstanding work and winners are chosen by a panel of experts. The resulting public exhibitions are always extremely popular and receive widespread acclaim. All images on the Wellcome Images site are available free for use in: * private study and non-commercial research * examination papers * criticism and review, this applies only where there are no multiple copies made * theses submitted by a student at a higher or further education institution for the purposes of securing a degree * personal use by private individuals

Proper citation: Wellcome Images (RRID:SCR_004181) Copy   

•   Source: SciCrunch Registry

http://datashare.ucsf.edu/

Platform to facilitate sharing, discovery, and secure access to UCSF biomedical data. It''s powered by the Dataverse Network platform, which supports a variety of data types, as well as attribution and licensing needs. Researchers may share datasets, discover data from other labs, and reuse data. Links to tools and information that help scientists properly organize, manage, and document their datasets are also provided.

Proper citation: UCSF DataShare (RRID:SCR_004340) Copy   

•   Source: SciCrunch Registry

https://brainspan.org/

Atlas of developing human brain for studying transcriptional mechanisms involved in human brain development. One of the BrainSpan datasets, Exon microarray summarized to genes, is presented. It is a downloadable archive of files containing normalized RNA-Seq expression values for analysis.

Proper citation: BrainSpan (RRID:SCR_004219) Copy   

•   Source: SciCrunch Registry

http://www.xenbase.org/anatomy/xao.do?method=display

A structured, controlled vocabulary of the anatomy and development of the African clawed frogs (Xenopus laevis and tropicalis), organized in a graphical structure. Tissues are shown as being part of other tissues and the timing of their development is indicated by start and end stages. The lineage of tissues is represented by develops from relationships between different tissues at different developmental stages. Many items have been classified according to the Common Anatomy Reference Ontology. The Xenopus Anatomical Ontology will be used to annotate Xenopus gene expression patterns and mutant and morphant phenotypes. Its robust developmental map will enable powerful database searches and data analyses. They encourage community recommendations for updates and improvements to the ontology.

Proper citation: Xenopus Anatomy Ontology (RRID:SCR_004337) Copy   

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http://neuroandpsych.slu.edu/

The Department of Neurology & Psychiatry aims to 1) provide the best psychiatric and neurological care to patients and their families, 2) discover and investigate new treatments for psychiatric and nervous system disorders, 3) study psychosocial processes in psychiatric and neurological illness, and 4) educate the next generation of practitioners, as well as our patients and the lay community. The Department of Neurology & Psychiatry (DNP) was established on June 1, 2007. The Department has 34 faculty members and is planning continued expansion. There are 7 psychiatrists, 18 neurologists, 4 child neurologists, and 5 NIH-supported PhD investigators. The DNP is one of five departments in the country that combines the disciplines of neurology and psychiatry. We are unique in having two strong residency programs and are the only that attempts to establish a new paradigm in care of patients with neurological and psychiatric disease through co-management initiatives. * Division of Psychiatry: The Psychiatrists work within four areas: Adult, Geriatric, Community, and Forensic Psychiatry. * Division of Neurology: The division has an extremely active stroke/intensive care and general neurology service. We are expanding services in neurocritical care and interventional neurology. * Education: The DNP has approximately 25 residents/fellows in each discipline. * Research: The DNP has robust programs in clinical, basic, and translational research. We emphasize 3 areas in this overview of the DNP. ** Clinical Research Unit ** Psychosocial Processes Group ** Translational Neuromuscular Disease VISION STATEMENT All members of the Saint Louis University Department of Neurology & Psychiatry will collaborate to support state-of-the-art neurological and psychiatric education, compassionate patient care, and a growing research enterprise. The Department will develop the most exciting intellectual environment in the Nation for investigation, treatment, and training in psychiatry and neurology. We will fulfill this Vision in an environment of mutual respect and collaboration.

Proper citation: St. Louis University Department of Neurology and Psychiatry (RRID:SCR_004297) Copy   

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http://bioinfo.au.tsinghua.edu.cn/software/TAGS/

Software tool for gene set enrichment analysis for expression time series, which can incorporate existing knowledge and analyze the dynamic property of a group of genes that have functional or structural associations. The installation file is for Windows., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: TAGS (RRID:SCR_004294) Copy   

•   Source: SciCrunch Registry

http://altbibl.io/dst4l/

An experimental course and blog offered by the Harvard-Smithsonian Center for Astrophysics John G. Wolbach Library and the Harvard Library to train librarians to respond to the growing data needs of their communities. Data science techniques are becoming increasingly important to all fields of scholarship. In the hands-on course, librarians learn the latest tools for extracting, wrangling, storing, analyzing, and visualizing data. By experiencing the research data lifecycle themselves, librarians develop the data savvy skills that can help transform the services they offer. Material will be made available via the DST4L website as it progresses.

Proper citation: Data Scientist Training for Librarians (RRID:SCR_004124) Copy   

•   Source: SciCrunch Registry