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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   

•   Source: SciCrunch Registry
  

http://www.dukecancerinstitute.org/

One of 40 centers in the country designated by the National Cancer Institute (NCI) as a comprehensive cancer center, it combines cutting-edge research with compassionate care. Its vision is to accelerate research advances related to cancer and improve Duke''s ability to translate these discoveries into the most advanced cancer care to patients by uniting hundreds of cancer physicians, researchers, educators, and staff across the medical center, medical school, and health system under a shared administrative structure.

Proper citation: Duke Cancer Institute (RRID:SCR_004338) Copy   

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http://www.netsci.org/

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   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/pasha/

A parallel short read assembler for large genomes using de Bruijn graphs.

Proper citation: PASHA (RRID:SCR_004455) Copy   

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http://neurobiology.informatics.sunysb.edu/

The Department of Neurobiology currently has 18 faculty with substantial research strengths in neural development, circuit function, computation, cellular communication through receptors, channels and synapses and neurological and psychiatric diseases. The Department offers a university-wide predoctoral training program designed to provide broad training opportunities for students interested in careers in the neurosciences. Students can enter from their undergraduate training or through the MD/PhD program. The graduate program provides a broad educational background in neurobiology, experience in teaching, and the opportunity to pursue original doctoral research in one of over 40 laboratories. The program includes scientists at SUNY Stony Brook, recently ranked number two in the Graham/Diamond study of public research institutions, at Cold Spring Harbor Laboratories, an internationally renowned private research institute, and at Brookhaven National Laboratory, a multidisciplinary research facility of the U.S. Department of Energy. Total research grant funding for the primary faculty of $6.8 million dollars was received in FY 2008. Under the direction of Dr. Lorna Role, who arrived as Chair in April 2008, the department looks forward to continued growth, expansion and innovation. If you consider yourself a Postdoc in training, regardless of your title, you are welcome to participate in our program.

Proper citation: Stony Brook University Department of Neurobiology and Behavior (RRID:SCR_004335) Copy   

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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   

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http://genie.weizmann.ac.il/software/nucleo_prediction.html

This tool allows you to submit a genomic sequence and to recieve a prediction of the nucleosomes positions on it, based on the nucleosome-DNA interaction model that we developed in these papers: * Segal et al., A Genomic Code for Nucleosome Positioning, Nature 2006 * Field et al., Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals, PLoS Comp Biol. 2008 * Kaplan et al., The DNA-Encoded Nucleosome Organization of a Eukaryotic Genome, Nature 2008 We recommend using the latest version of the model (Version 3), which is applicable to all species. Paste in a sequence to analyze or upload file. You can provide multiple sequences in fasta format (separate sequences by lines starting with ''>'' followed by the sequence name). The length of each sequence must be between 147bp and 40kb bp. Note: Due to boundary effects, we highly recommend that you add at least 5000 bp of flanking sequence around your sequence of interest. You can generate the nucleosomes positioning predictions on your own machine using our executable and wrapping Perl scripts.

Proper citation: Online Nucleosomes Position Prediction by Genomic Sequence (RRID:SCR_004210) Copy   

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http://www.qub.ac.uk/schools/BioimagingCoreTechnologyUnit/NIVTA/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. A pan European network for virtual tissue archiving aimed at supporting clinical trials, biomarker research, tissue microarray analysis and virtual slide based education. NIVTA has state-of-the-art digital scanning systems including an Aperio CS system, Aperio OS system (one of only two currently available in Europe) and a Hamamatsu system with fluorescent scanning capability.

Proper citation: Northern Ireland Virtual Tissue Archive (RRID:SCR_004452) Copy   

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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   

•   Source: SciCrunch Registry
  

http://www.genopole.fr/?lang=en

Genopole is France''s leading biotech-and biotherapy-dedicated science and business park. The Genopole project was initiated in 1998 in the town of Evry-Corbeil, under the impetus of the French government, Ile-de-France Regional Council, Essonne County Council and the French Muscular Dystrophy Association (Association Francaise contre les Myopathies, AFM); the goal was to create France''s first ever science and business park dedicated to genomics, genetics and biotech and help the country to catch up with its international rivals in these fields. Its threefold mission is 1. to develop a high-level research campus in genomics and post-genomics, focused on gene therapy in collaboration with the University Evry Val d''Essonne; 2. encourage the start-up and foster the development of biotech companies in the Paris region by providing personalized advice and support, including financial assistance and 3. create a biopark in Evry-Corbeil in collaboration with the research campus. In addition to constant support from its founding members and other partners, Genopole''s success is largely based on the novelty of its approach: bringing together public-and private-sector research labs, university teaching facilities and life science start-ups on a single campus in EvryCorbeil. In collaboration with France''s national research institutes and the Paris Ile-de-France region''s universities, Genopole hosts and equips academic research units specializing in genetics, genomics and related sciences. Genopole also stimulates scientific life on the biopark by coordinating and organizing high-level teaching & training programs, seminars, symposia, business clubs and much more.

Proper citation: Genopole (RRID:SCR_004333) Copy   

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http://noble.gs.washington.edu/proj/svmvia/

Software that implements the full regularization path optimization algorithm for training a support vector machine. The support vector machine algorithm has a single hyperparameter C that regularizes the learned model. Recently, Hastie et al. (2004) described an algorithm for finding the SVM solution for all possible values of this regularization parameter. An efficient C++ implementation of this algorithm is presented. For large values of C, it is often faster to find the entire regularization path than to train a single model.

Proper citation: svmvia (RRID:SCR_004209) Copy   

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http://www.epilepsy.ie/index.cfm/spKey/research.html

Epilepsy Research Ireland is a non-profit organization (Charity CHY17527), run by a group of volunteers, who are dedicated to find cure for epilepsy by raising awareness and money for research. We can say cure now with much more confidence than we could even 10 years ago because recent advances in genetics, brain imaging and drug therapy, all hold out the promise of that holy grail the cure. We can also say with confidence that you can be part of that push by participating in this new foundation since we have collaborations with doctors and scientists all over Europe, the US and Australia, all of whom share the same goal. Epilepsy research, conducted by Epilepsy Research Ireland, is essential and will deliver benefits across the board. Research planned and already underway by Epilepsy Research Ireland will help develop and improve clinical skills; it will provide a knowledge base to develop new ways to manage and treat epilepsy; it will help in the evaluation of new medical advances. Ultimately we can improve the quality of care and provide greater understanding, better and more accurate diagnosis and more tailored treatments. Ireland is uniquely well-positioned, given its relatively homogenous population to make the goal, of making real discoveries in epilepsy research that will directly improve the lives of people with epilepsy, a realistic one.

Proper citation: Epilepsy Research Ireland (RRID:SCR_004448) Copy   

•   Source: SciCrunch Registry
  

http://figshare.com/

Repository for all data, figures, theses, publications, posters, presentations, filesets, videos, datasets, negative data in a citable, shareable and discoverable manner with Digital Object Identifiers. Allows to upload any file format to be made visualisable in the browser so that figures, datasets, media, papers, posters, presentations and filesets can be disseminated in a way that the current scholarly publishing model does not allow. Features integration with ORCID, Symplectic Elements, can import items from Github and is a source tracked by Altmetric.com. Figshare gives users unlimited public space and 1GB of private storage space for free. Data are digitally preserved by CLOCKSS. Supported by Digital Science, a division of Macmillan Publishers Limited, as a community-based, open science project that retains its autonomy.

Proper citation: FigShare (RRID:SCR_004328) Copy   

•   Source: SciCrunch Registry
  

http://www.cellmarque.com/

An Antibody supplier

Proper citation: Cell Marque (RRID:SCR_004449) Copy   

•   Source: SciCrunch Registry
  

http://www.nature.com/neurosci/neuropod/index.html

NeuroPod is the neuroscience podcast from Nature, produced in association with the Dana Foundation. Each month, join us as we delve into the latest research on the brain, from its molecular makings to the mysteries of the mind. We''ll also be bringing you the latest news from neuroscience conferences around the globe, along with special reports on hot areas in neuroscience.

Proper citation: NeuroPod (RRID:SCR_004329) Copy   

•   Source: SciCrunch Registry
  

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   

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http://www.uncc.edu/

Public research university in Charlotte, North Carolina.

Proper citation: University of North Carolina at Charlotte; North Carolina; USA (RRID:SCR_004244) Copy   

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http://www.tissuenet.com/

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   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

http://www.grissom.gr/stranger/

StRAnGER (Statistical Ranking of ANotated Genomic Experimental Results) is a web application for the automated statistical analysis of annotated gene profiling experiments, exploiting controlled biological vocabularies, like the Gene Ontology or the KEGG pathways terms. Starting from annotated lists of differentially expressed genes StRAnGER repartitions and reorders the initial distribution of terms to define a new distribution of elements where each element pools terms holding the same enrichment score. The elements are then prioritized according to StRAnGER''''s algorithm and, by applying bootstrapping techniques, a corrected measure of the statistical significance of these elements is derived, enabling the selection of terms mapped to these elements, unambiguously associated with respective significant gene sets. Besides their high statistical score, another selection criterion for the terms is the number of their members, something that incurs a biological prioritization in line with a Systems Biology context. Platform: Online tool

Proper citation: StRAnGER (RRID:SCR_004247) Copy   

•   Source: SciCrunch Registry