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http://www.msdiscovery.org/

Portal that aims to inspire connections, clinical advances and accelerate progress toward multiple sclerosis cures. MSDF updates its site with news and information about topics relevant to multiple sclerosis and hosts discussions about controversial subjects with the goal of spreading information and enabling collaboration between researchers. MSDF provides access to drug development pipelines, tissue repositories, the MS gene, animal models, and clinical trials.

Proper citation: Multiple Sclerosis Discovery Forum (RRID:SCR_000027) Copy   

•   Source: SciCrunch Registry
  

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

Software homology search tool for huge short reads generated by next-generation sequencers.Can detect remote homologs like BLAST and is about 40 times more efficient than BLAST by using a GPU-computing technique.

Proper citation: GHOSTM (RRID:SCR_000062) Copy   

•   Source: SciCrunch Registry
  

http://www.coloradocollege.edu/academics/dept/psychology/

A department within Colorado College that is dedicated to providing academic programs for undergraduate education. Students are educated in a variety of research techniques, statistics and design experiments.

Proper citation: Colorado College Department of Psychology (RRID:SCR_000063) Copy   

•   Source: SciCrunch Registry
  

https://code.google.com/p/primer-design/

An open-source C++ software library of classes for the design and analysis of primers suitable for a wide range of PCR applications.

Proper citation: PD5 (RRID:SCR_000068) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/mysirna/

Software that integrates several factors in an automated work-flow considering mRNA transcripts variations, siRNA and mRNA target accessibility, and both near-perfect and partial off-target matches.

Proper citation: MysiRNA-designer (RRID:SCR_000102) Copy   

•   Source: SciCrunch Registry
  

https://biomedia.doc.ic.ac.uk/software/mirtk/

Software image processing toolkit. Provides collection of libraries and command-line tools to assist in processing and analyzing imaging data. Used for adult and neonatal brain MR image registration, including rigid, affine, and non-rigid transformations, as well as reconstruction of cortical surface meshes.

Proper citation: Image Registration Toolkit (RRID:SCR_000067) Copy   

•   Source: SciCrunch Registry
  

http://www.ngsbicocca.org/html/fusion_analyser.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16, 2023. Software used to detect gene fusions from paired-end RNA-Seq data.

Proper citation: Fusion Analyser (RRID:SCR_000059) Copy   

•   Source: SciCrunch Registry
  

http://bioconductor.org/packages/release/bioc/html/CorMut.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Software package for computing correlated mutations based on selection pressure. Three methods are provided for detecting correlated mutations, including conditional selection pressure, mutual information and Jaccard index. The computation consists of two steps: First, the positive selection sites are detected; second, the mutation correlations are computed among the positive selection sites. Note that the first step is optional. Meanwhile, CorMut facilitates the comparison of the correlated mutations between two conditions by the means of correlated mutation network.

Proper citation: CorMut (RRID:SCR_000053) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/release/bioc/html/flowBin.html

A software package to combine flow cytometry data that has been multiplexed into multiple tubes with common markers between them. It establishes common bins across tubes in terms of the common markers, then determines expression within each tube for each bin in terms of the tube-specific markers.

Proper citation: flowBin (RRID:SCR_000051) Copy   

•   Source: SciCrunch Registry
  

http://projects.kmi.open.ac.uk/scholonto/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 25,2022. Project (2001-2004) to build and deploy a prototype infrastructure for making scholarly claims about the significance of research documents. "Claims" are made by making connections between ideas. Any claim is open to counterarguments. The connections are grounded in a discourse/argumentation ontology, which makes possible innovative services for navigating, visualizing and analyzing the network as it grows. They have evolved a suite of prototype tools for modelling conceptual networks of ideas and arguments, publishing them for reuse and argumentation, and navigating, searching and filtering this repository as it grows. Some of these are freely available to play with, but WARNING! they are no longer able to support them. The system they have built is called ClaiMaker. Others include ClaimSpotter, ClaiMapper, ClaimFinder, ClaimBlogger and ClaiMaker Microsoft Word plug-in. Additionally, the ScholOnto RDF Schema is available, http://projects.kmi.open.ac.uk/scholonto/resources/Scholonto2.rdfs User Communities: They envisage such a tool as having potential not only in scholarly publishing, but for corporate knowledge analysis, and in education. Complementary work: ScholOnto's focus on net-centric representations of research is complemented by work on augmenting more conventional textual documents, with threaded commentary and debate. An open source web publishing tool is available called D3E (Digital Document Discourse Environment). Many applications are illustrated on the site, including the award-winning Journal of Interactive Media in Education.We are no longer able to support tools, so are not able to assist if you have problems or lose data.

Proper citation: Scholarly Ontologies Project (RRID:SCR_000057) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/release/bioc/html/metaSeq.html

Software package for meta-analysis of RNA-Seq count data in multiple studies. The probabilities by one-sided NOISeq are combined by Fisher's method or Stouffer's method.

Proper citation: metaSeq (RRID:SCR_000056) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/dprimer/

A command line software utility for designing degenerate PCR primers against multiple, aligned sequences. Its primary use case is searching for a family of related pathogens in a host tissue sample.

Proper citation: dprimer (RRID:SCR_000050) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/imethy/

Software for investigation and visualization of DNA methylation by high-throughput bisulfite sequencing.

Proper citation: iMethy (RRID:SCR_000049) Copy   

•   Source: SciCrunch Registry
  

http://www.komp.org/

Repository of mouse vectors, ES cells, mice, embryos, and sperm generated by NIH KOMP Mutagenesis Project. In addition, KOMP Repository offers services in support of KOMP products, including ES cell microinjection, vector cloning, post-insertional modification of cloned ES cells, cryopreservation, assisted reproduction techniques (IVF, ICSI) and mouse breeding, pathology services, phenotyping services, etc. KOMP Repository is final component of more than $50 million trans-NIH initiative to increase availability of genetically altered mice and related materials. The University of California, Davis (UC Davis) and Children''s Hospital Oakland Research Institute (CHORI) in Oakland, Calif., are collaborating to preserve, protect, and make available about 8,500 types of knockout mice and related products available to research community. Products are generated by two KOMP mutagenesis teams (CSD consortium and Regeneron Inc). All KOMP products generated by CSD consortium and Regeneron are available through KOMP Repository. Notice as of December 19, 2019: Materials from KOMP Repository have been deposited into MMRRC, including all mouse models and mouse embryonic stem cell lines. Eventually www.komp.org will be sunsetting, and IMSR will remove KOMP Repository listings, since they were double listed in MMRRC. MMRRC will contain the most accurate and up to date resource models.

Proper citation: Knockout Mouse Project Repository (RRID:SCR_007318) Copy   

•   Source: SciCrunch Registry
  

http://www.neuroinf.de

Portal used to coordinate activities of the German portion of the INCF group. The main focus is the development and free distribution of software tools for handling and analyzing neurophysiological data.

Proper citation: German Neuroinformatics Node (G-Node) (RRID:SCR_007279) Copy   

•   Source: SciCrunch Registry
  

http://www.aptcenter.research.va.gov/aptcenterresearch/

Software and hardware core facility supporting clinical investigators at VA Research Center at Case Western Rserve University. The APT Center is a VA Research Center of Excellence established January 2005 in partnership with Case Western Reserve University. Clinicians, investigators, and staff work together to bring the clinical needs of veterans to the attention of the engineers and scientists pursuing new and emerging technologies in order to apply them for the purposes of reducing disability, improving daily functions, and enhancing quality of life. We are a technical center that designs and builds prototype devices that are clinically meaningful. We support rehabilitation research by adapting cross-cutting foundational technical platforms to meet specific needs for advanced prosthetic systems, sensory aids, and other clinical applications. Most grant-supported research concentrates on system development, pre-clinical testing, and clinical studies. The APT Center focuses on other aspects of the device development cycle, specifically: 1 the identification of user needs, 2 the generation of new concepts (innovation), 3 the development of new technologies through prototype and intial fabrication stages By shifting our focus, we are able to provide support to other Centers of Excellence when they need novel technologies or reach the point of technology transfer. List of projects the APT Center is attempting to undertake: Clinical needs assessment, Novel technologies to accelerate wound healing, Subcutaneous myoelectric signal (EMG) telemeter for prosthetic control, Switchable polymer materials that match their properties to the body, MEMS based implantable pressure sensors, Integrated control and sensory feedback for powered limb prostheses, Networked neural prostheses grants, funding.

Proper citation: Advanced Platform Technology Center (RRID:SCR_007396) Copy   

•   Source: SciCrunch Registry
  

http://www.alz.org/

A non profit organization dedicated to providing support for patients and families with Alzheimer's disease, to educating the public about the disease, to funding a wide range of Alzheimer's disease related research and to finding ways to treat and eventually to prevent Alzheimer's disease. Resources include: the Alzheimer's Association Green-Field Library, a research grants program, and the Journal of the Alzheimer's Association.

Proper citation: Alzheimers Association (RRID:SCR_007398) Copy   

•   Source: SciCrunch Registry
  

http://www.alzdiscovery.org

The Alzheimers Drug Discovery Foundation (ADDF) is the only public charity whose sole mission is to accelerate the discovery and development of drugs to prevent, treat and cure Alzheimers disease, related dementias and cognitive aging. Founded in 1998 by the Este Lauder family, the ADDF awards grants to leading scientists conducting breakthrough drug discovery research. We use a venture philanthropy model to bridge the worldwide funding gap between basic research and later-stage drug development, using any return on investment to support new research. We have granted more than 40 million to fund over 295 Alzheimers drug discovery programs in academic centers and biotechnology companies in 15 countries. Scientists funded by the ADDF have entered clinical trials with several new drugs. The ADDF has invested over 8 million in 40 biotechnology companies, which have received follow-on commitments of over 1 billion. Keywords: Research, Funding, Alzheimer''s, Drug, Discovery, Biotechnology, Biomedical, Development, Investment, Prevention, Treatment, Cure, Cognitive, Aging, Dementia, Disease,

Proper citation: Alzheimers Drug Discovery Foundation (RRID:SCR_007397) Copy   

•   Source: SciCrunch Registry
  

http://senselab.med.yale.edu/modeldb/

Curated database of published models so that they can be openly accessed, downloaded, and tested to support computational neuroscience. Provides accessible location for storing and efficiently retrieving computational neuroscience models.Coupled with NeuronDB. Models can be coded in any language for any environment. Model code can be viewed before downloading and browsers can be set to auto-launch the models. The model source code has to be available from publicly accessible online repository or WWW site. Original source code is used to generate simulation results from which authors derived their published insights and conclusions.

Proper citation: ModelDB (RRID:SCR_007271) Copy   

•   Source: SciCrunch Registry
  

http://www.neuropat.dote.hu/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 07, 2013. A set of human neuroanatomical resources developed at the University of Hungary. Resources include an on-line brain atlas, a neuropathology atlas, functional neuroanatomy for neurologists and an extensive series of links to other neuroanatomy and neurological resources on the web. The original resources developed by this site include a set of neuropathological slides covering many neurological conditions, e.g., Alzheimer's disease, an atlas of normal human neuroanatomy based on unstained brain slices, along with histological images of brainstem and spinal cord. On-line quizzes are also provided. This is an excellent educational site and gateway to neurological resources on the web.

Proper citation: Neuroanatomy and Neuropathology on the Internet (RRID:SCR_007272) Copy   

•   Source: SciCrunch Registry