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https://github.com/dsturg/Spanki
A set of tools to facilitate analysis of alternative splicing from RNA-SEQ data.
Proper citation: Spanki (RRID:SCR_004469) Copy
http://www.brainnet-europe.org/
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 7, 2022. Consortium of 19 brain banks across Europe with an aim to harmonize neuropathological diagnostic criteria and develop gold standards for quality, safety and ethics standards for brain banking. BrainNet Europe also contributes to research on rare diseases, such as: Pick''s disease or other rare forms of dementia, as well as to questions after the events in the aging brain. Anyone can be a donor - irrespective of disease of the central nervous system or not, because for research purposes, one does not only need tissue samples from ill donors, but also from healthy ones for comparison.
Proper citation: BrainNet Europe (RRID:SCR_004461) Copy
Scientific focus articles and general resources for scientists within the pharmaceutical and biotechnology industries that take a comprehensive look at the industry and the tools that are in use to speed drug discovery and development. Resources include a forum, courseware, and a listing of professional societies, associations and companies/organizations. In addition to features on classical drug discovery, NetSci will address biotechnology, genomic research, and materials design as well as subjects suggested by readers. Network Science has collected an extensive list of professional societies and associations and companies/organizations that are a part of the world-wide efforts in drug discovery and development. These organizations were selected based upon the fact that they contribute to pharmaceutical research and development and healthcare throughout the world. The forum for experts to explore and discuss current applications of science and technology with their colleagues world-wide, permits publication of scientific data without the delays inherent in traditional printed media and encourages immediate dialog using hypertext (a contextual linkage of related information sources), multimedia, interactive electronic feedback forms, and automatic electronic mail connections which are not available within any other media. CourseWare provides a collection of materials which examine the pharmaceutical industry and the use of technology in drug discovery. Topics range from an introduction to the drug development process to an in-depth examination of the tools and techniques used in pharmaceutical research and development. If your would like to see a topic added to this collection, or know about companies and products that you feel would be of interest to the readers, would like to add your organization to the list or correct the listing that is on-line, please contact us.
Proper citation: Network Science (RRID:SCR_004459) Copy
http://sourceforge.net/projects/pasha/
A parallel short read assembler for large genomes using de Bruijn graphs.
Proper citation: PASHA (RRID:SCR_004455) Copy
http://www.leonxie.com/DeepFinder.php
Provides an comprehensive workflow of analyzing data from plant microRNA (miRNA) deep sequencing.
Proper citation: miRDeepFinder (RRID:SCR_004456) Copy
http://discovery.hsci.harvard.edu/
An online database of curated cancer stem cell (CSC) experiments coupled to the Galaxy analytical framework. Driven by a need to improve our understanding of molecular processes that are common and unique across cancer stem cells (CSCs), the SCDE allows users to consistently describe, share and compare CSC data at the gene and pathway level. The initial focus has been on carefully curating tissue and cancer stem cell-related experiments from blood, intestine and brain to create a high quality resource containing 53 public studies and 1098 assays. The experimental information is captured and stored in the multi-omics Investigation/Study/Assay (ISA-Tab) format and can be queried in the data repository. A linked Galaxy framework provides a comprehensive, flexible environment populated with novel tools for gene list comparisons against molecular signatures in GeneSigDB and MSigDB, curated experiments in the SCDE and pathways in WikiPathways. Investigation/Study/Assay (ISA) infrastructure is the first general-purpose format and freely available desktop software suite targeted to experimentalists, curators and developers and that: * assists in the reporting and local management of experimental metadata (i.e. sample characteristics, technology and measurement types, sample-to-data relationships) from studies employing one or a combination of technologies; * empowers users to uptake community-defined minimum information checklists and ontologies, where required; * formats studies for submission to a growing number of international public repositories endorsing the tools, currently ENA (genomics), PRIDE (proteomics) and ArrayExpress (transcriptomics). Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignments, compare genomic annotations, profile metagenomic samples and much much more. Best of all, Galaxy''''s history system provides a complete analyses record that can be shared. Every history is an analysis workflow, which can be used to reproduce the entire experiment. The code for this Galaxy instance is available for download from BitBucket.
Proper citation: Stem Cell Discovery Engine (RRID:SCR_004453) Copy
http://rarediseasesnetwork.epi.usf.edu/STAIR/index.htm
A consortium which represents a collaborative group of investigators along with their academic medical centers and the National Institutes of Health, patient advocacy groups, and clinical research programs. Members of the STAIR Consortium are dedicated to participating in clinical research regarding disorders related to cholesterol and other sterol and isoprenoid metabolism. The overall objective of the Sterol and Isoprenoid Research Consortium (STAIR) is to study a group of diseases bound by common biochemistry, impact on health, and rarity. STAIR will conduct several clinical studies, support a full-scale training program in the field of sterol and isoprenoid diseases, and engage several patient advocacy groups in consortium activities. Researchers interested in partnering with STAIR may contact its Administrative Director.
Proper citation: Sterol and Isoprenoid Research Consortium (RRID:SCR_004367) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 17,2021. Manufacturer of allograft tissue grafts in the United States in the ortho-biologics field of medicine. They develop new products for the patients they serve, including the UltraGraft non-irradiated & sterile line of allograft tissue implants., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: TissueNet (RRID:SCR_004489) Copy
http://mged.sourceforge.net/ontologies/MGEDontology.php
An ontology including concepts, definitions, terms, and resources for a standardized description of a microarray experiment in support of MAGE v.1. The MGED ontology is divided into the MGED Core ontology which is intended to be stable and in synch with MAGE v.1; and the MGED Extended ontology which adds further associations and classes not found in MAGE v.1. These terms will enable structure queries of elements of the experiments. Furthermore, the terms will also enable unambiguous descriptions of how the experiment was performed.
Proper citation: MGED Ontology (RRID:SCR_004484) Copy
http://www.onr.navy.mil/en.aspx
Organization within the United States Department of the Navy responsible for the science and technology programs of the U.S. Navy and Marine Corps.
Proper citation: Office of Naval Research (RRID:SCR_004366) Copy
Founded in 1551, this research university features murals by Diego Rivera and other famous artists.
Proper citation: National Autonomous University of Mexico; Mexico City; Mexico (RRID:SCR_004360) Copy
http://virome.diagcomputing.org/#view=home
A web-application designed for scientific exploration of metagenome sequence data collected from viral assemblages occurring within a number of different environmental contexts. The VIROME informatics pipeline focuses on the classification of predicted open-reading frames (ORFs) from viral metagenomes. The portal allows you to submit your viral metagenome to be processed through the VIROME analysis pipeline, and enable you to investigate your data via the VIROME user interface., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: VIROME (RRID:SCR_004362) Copy
http://vamps.mbl.edu/overview.php
A publicly-accessible website to measure and visualize similarities and differences between molecular profiles of complex microbial communities. The project includes visualization tools such as heat maps that simultaneously compare the taxonomic distributions of multiple datasets and 3-D charts of the frequency distributions of 16S rRNA tags. Analytical tools include Chao diversity estimates and rarefaction curves. As a service to the community, researchers have the opportunity to upload their own data to the site for private viewing with the full range of data and analysis tools. Public data can be downloaded for further analysis locally.
Proper citation: VAMPS (RRID:SCR_004483) Copy
http://www.hcp.med.harvard.edu/wmh/
The WMH Survey Initiative is a project of the Assessment, Classification, and Epidemiology (ACE) Group at the World Health Organization coordinating the implementation and analysis of general population epidemiologic surveys of mental, substance use, and behavioral disorders in countries in all WHO Regions. Reported are the first results of the WHO World Mental Health (WMH) Survey Initiative, a highly ambitious series of cross-national psychiatric epidemiological surveys. The general population surveys in the WMH series span 17 countries in all parts of the world. In many of these countries the WMH surveys provide the first community epidemiological data ever available on mental disorders in the population. The detailed information on lifetime prevalence, age of onset, course, correlates, and treatment of mental disorders in this volume provides mental health professionals and healthcare policy planners with an unprecedented reference on the cross-national descriptive epidemiology of mental disorders. The WHO Global Burden of Disease Study estimates that mental and addictive disorders are among the most burdensome in the world and their burden will increase over next decades. However, these estimates and projections are based largely on literature reviews and limited and isolated studies rather than on cross-national epidemiologic surveys. In order to move forward with public health initiatives aimed at addressing the global burden of mental disorders the WMH Survey Initiative carried out rigorously implemented general population surveys that estimate the prevalences of mental disorders, evaluate risk factors for purposes of targeting interventions, study patterns of and barriers to service use, and validate estimates of disease burden world-wide. The WMH Survey Initiative aims to obtain accurate cross-national information about the prevalences and correlates of mental, substance, and behavioral disorders. Included in studies of correlates will be analyses of impairments, other adverse social consequences, and patterns of help-seeking. The WMH Survey Consortium includes nationally or regionally representative surveys in 28 countries, representing all regions of the world, and with a total eventual sample size in excess of 154,000. ISBN:9780521884198
Proper citation: WHO World Health Mental Health Surveys (RRID:SCR_004511) Copy
EuPathDB integrates numerous database resources and multiple data types. The phylum Apicomplexa comprises veterinary and medically important parasitic protozoa including human pathogenic species of genera Cryptosporidium, Plasmodium and Toxoplasma. ApiDB serves not only as database but unifies access to three major existing individual organism databases, PlasmoDB.org, ToxoDB.org and CryptoDB.org, and integrates these databases with data available from additional sources. Through ApiDB site, users may pose queries and search all available apicomplexan data and tools, or they may visit individual component organism databases. EuPathDB Bioinformatics Resource Center for Biodefense and Emerging/Re-emerging Infectious Diseases is a portal for accessing genomic-scale datasets associated with eukaryotic pathogens.
Proper citation: Eukaryotic Pathogen Database Resources (RRID:SCR_004512) Copy
Intergovernmental organisation funded by public research money from its member states in Europe. Groups and laboratories perform basic research in molecular biology and molecular medicine, training for scientists, students and visitors. Provides development of services, new instruments and methods, data and technology in its member states.
Proper citation: European Molecular Biology Laboratory (RRID:SCR_004473) Copy
Public, high-value federal datasets, tools, and applications using data about health and health care gathered from agencies across the U.S. government.
Proper citation: Health.Data.gov (RRID:SCR_004386) Copy
http://snoopcgh.sourceforge.net/
A java desktop application for visualising and exploring comparative genomic hybridization (CGH) data.
Proper citation: SnoopCGH (RRID:SCR_004420) Copy
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