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http://neuro.imm.dtu.dk/wiki/Main_Page

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 10, 2025. Semantic wiki with structured information, primarily from functional and molecular neuroimaging papers, but there are also other types of papers, e.g., from personality genetics. It lists results from neuroimaging studies, such as Talairach coordinates and brain volume measurements, as well as software packages and brain regions. SQL dumps of the structured information in the wiki is available so complex queries can be formed. The Brede Wiki templates store the structured information from neuroscience papers and editors may add free format text. Template definitions format the data so it is presented as tables on the formatted wiki-page. From a given PMID a web-service can format information from PubMed for inclusion in the Brede Wiki. A Matlab script can extract coordinates from SPM5 and format them in the Talairach coordinate template format.

Proper citation: Brede Wiki (RRID:SCR_001411) Copy   

•   Source: SciCrunch Registry

https://omictools.com/splitseek-tool

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 20, 2016. A program for de novo prediction of splice junctions in RNA-seq data.

Proper citation: SplitSeek (RRID:SCR_001012) Copy   

•   Source: SciCrunch Registry

http://www.g-node.org/projects/odml

Mark up language for collecting and exchanging metadata in an automated, computer-based fashion, developed for neuroscience, specifically, neurophysiology experiments. In odML arbitrary metadata information is stored as extended key-value pairs in a hierarchical structure. Central to odML is a clear separation of format and content, i.e., neither keys nor values are defined by the format. This makes odML flexible enough for storing all available metadata instantly without the necessity to submit new keys to an ontology or controlled terminology. Common standard keys can be defined in odML-terminologies for guaranteeing interoperability.

Proper citation: Open metadata mark up language (RRID:SCR_001376) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/jmosaics.html

R software that detects enriched regions of ChIP-seq data sets jointly.

Proper citation: Jmosaics (RRID:SCR_001094) Copy   

•   Source: SciCrunch Registry

http://sun.aei.polsl.pl/gdc/

A C++ application designed for compression of genome collections from the same species.

Proper citation: GDC (RRID:SCR_001007) Copy   

•   Source: SciCrunch Registry

http://www.softgenetics.com/mutationSurveyor.php

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for DNA sequencing analysis that integates with Sanger Sequencing files generated by Applied Biosystems Genetic Analyzers, MegaBACE, and Beckman CEQ electrophoresis systems. It can be used to find single nucleotide polymorphisms (SNPs), insertions and deletions (INDELS), and somatic mutations in direct sequencing, PCR sequencing, mitochondrial DNA sequencing, and resequencing projects.

Proper citation: Mutation Surveyor (RRID:SCR_001247) Copy   

•   Source: SciCrunch Registry

http://ausweb.scu.edu.au/aw06/papers/refereed/sefton/paper.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The Integrated Content Environment (ICE) is a free Word-processor based system that allows authors to work individually or collaboratively on material for the Web, CD and print. This free web content management system, produced by the University of Southern Queensland, was initially developed by staff at the university to produce course content for online and print delivery. It has also been used for general web site development, and to manage documents in project intranets.

Proper citation: Integrated Content Environment (RRID:SCR_001369) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/autoassemblyd/

Software which performs local and remote genome assembly by several assemblers based on an XML Template which can replace the large command lines required by most assemblers.

Proper citation: AutoAssemblyD (RRID:SCR_001087) Copy   

•   Source: SciCrunch Registry

http://www.genome.jp/kegg/expression/

Database for mapping gene expression profiles to pathways and genomes. Repository of microarray gene expression profile data for Synechocystis PCC6803 (syn), Bacillus subtilis (bsu), Escherichia coli W3110 (ecj), Anabaena PCC7120 (ana), and other species contributed by the Japanese research community.

Proper citation: Kyoto Encyclopedia of Genes and Genomes Expression Database (RRID:SCR_001120) Copy   

•   Source: SciCrunch Registry

http://scitools.idtdna.com/analyzer/Applications/OligoAnalyzer/

Web-based application for analyzing oligonucleotides. Analysis proceeds after the sequence has been entered and the calculations modified based on target type, oligo concentration, sodium ion concentration, magnesium ion concentration, and dNTP concentration.

Proper citation: Integrated DNA Technologies OligoAnalyzer (RRID:SCR_001363) Copy   

•   Source: SciCrunch Registry

https://www.unafold.org/

Software package for nucleic acid folding and hybridization prediction. It has capabilities to predict folding for single-stranded RNA or DNA through a combination of free energy minimization, partition function calculations and stochastic sampling. The program runs on Unix and Linux platforms as well as Mac OS X and Windows.

Proper citation: UNAFold (RRID:SCR_001360) Copy   

•   Source: SciCrunch Registry

http://isp.imm.dtu.dk/thor/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.Center hosting a number of related projects concerning neural networks, functional neuroimaging, multimedia signal processing, and biomedical signal processing. Neuroinformatics is a research field rooted in classical disciplines like signal processing, biology, physics, computer science and engineering. Neuroinformatics combines learning from the brain and learning about the brain. By studying information processing in the brain neuroinformatics invents new computing paradigms (e.g., artificial neural networks) with the objective of understanding the dynamics of the conscious mind. Artificial neural networks is an active neuroinformatics research field, which combines many approaches to adaptive signal processing in solving real world problems. They began using neural networks for general nonlinear adaptive signal processing. Since 1991 the CONNECT groups have participated in the development of neural computing as an advanced, non-linear statistical tool, which has been applied to forecasting within dynamical systems, pattern recognition, and medical image analysis, particularly functional neuroimages. While neural computing has largely been viewed as a black box approach, they have initiated research aimed at opening this black box, using hypertext, multimedia, and interactivity. Their key objective is to convert abstract models into intuitive knowledge through interactive visualization.

Proper citation: THOR Center for Neuroinformatics (RRID:SCR_001400) Copy   

•   Source: SciCrunch Registry

http://www.neuroscience.ufl.edu/

A department at the University of Florida's College of Medicine that offers programs of study on neural function and how it changes with injury and disease. The institution's research ranges from fundamental discovery to clinical application. These neuroscience programs are offered at the undergraduate, graduate, postdoctoral and resident level.

Proper citation: University of Florida College of Medicine Neuroscience (RRID:SCR_001081) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/macquarie-university

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. Set of facilities based out of Macquarie University in New South Wales. Some facilities provide services such as proteome analysis or resources of various academic departments like engineering, biological sciences, and geography.

Proper citation: Macquarie University Labs and Facilities (RRID:SCR_000944) Copy   

•   Source: SciCrunch Registry

http://www.well.ox.ac.uk/happy/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package for Multipoint QTL Mapping in Genetically Heterogeneous Animals (entry from Genetic Analysis Software) The method is implemented in a C-program and there is now an R version of HAPPY. You can run HAPPY remotely from their web server using your own data (or try it out on the data provided for download).

Proper citation: Happy (RRID:SCR_001395) Copy   

•   Source: SciCrunch Registry

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

Software package to load, manipulate, and plot copynumber and BAF data by providing classes similar to ExpressionSet for copy number analysis. The class extends ExpressionSet by adding a locData slot for a RangedData or GRanegs object. This object contains feature genome location data and provides for efficient subsetting on genome location. CNSet and BAFSet extend GenoSet and require assayData matrices for Copy Number (cn) or Log-R Ratio (lrr) and B-Allele Frequency (baf) data. Implements and provides convenience functions for processing of copy number and B-Allele Frequency data.

Proper citation: GenoSet (RRID:SCR_001275) Copy   

•   Source: SciCrunch Registry

http://www.ciscrp.org

CISCRP is a resource for information on participation in, understanding of, and resources for clinical research participants and scientists. The mission of the Center is to educate, inform and empower patients, the public, medical and research professionals, the media and policymakers about clinical research participation and what it means to be an active participant in the clinical research process, promote greater awareness and understanding of clinical research participation and the role that it plays in public health, facilitate more effective collaboration among all members of the clinical research enterprise, and provide resources for the research community to better understand the study volunteer. To that end, the Center has developed a broad national awareness and education initiative in order to better inform the public at large about clinical study information. Furthermore, on its website, the Center offers program and event information related to clinical trials, an information center with facts, figures, informational resources, and FAQs for both patients and researchers, and a mailing list of clinical trial information. :The Center also maintains its own search engine website, : :searchclinicaltrials.org : : :, for those looking for further clinical trial information. The Center for Information and Study on Clinical Research Participation is located in Dedham, MA. :NIF thanks the : :Parkinson's Disease Foundation : : :for their referral of this resource to us.

Proper citation: CISCRP- The Center for Information and Study on Clinical Research Participation (RRID:SCR_001152) Copy   

•   Source: SciCrunch Registry

http://www.retinalmaps.com.au/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A database of over 700 retinal topography maps of a wide variety of species published in a diversity of journals. It has been assembled to assist vision and neuroscience researchers to locate and compare the distribution of retinal neurons within and across species. The maps can be searched by taxonomic or common name classification, cell type sampled, type of retinal specialization and staining/visualization method. Maps can be compared by selecting multiple maps and clicking the Compare Selected button. An interactive spreadsheet can be also downloaded.

Proper citation: Retinal Topography Maps Database (RRID:SCR_001399) Copy   

•   Source: SciCrunch Registry

http://www.centerwatch.com

CenterWatch is an online resource for news, directories, analysis, and proprietary market research for clinical research professionals and patients. For patients, CenterWatch is committed to providing information on clinical trials, specific drugs, as well as other essential health and educational resources. On this website, patients can search clinical trials, receive e-mail notifications about specific clinical trials, review results from completed clinical trials, search drug information, learn about volunteering for a clinical trial, read an overview of the clinical trials process and find other health and educational resources. For researchers, CenterWatch offers a wide range of tools and resources to improve patient and investigator recruitment, remain current with industry trends and business practices, and strengthen organizational procedures. CenterWatch also offers information on grant opportunities, and a variety of educational books and publications. Researchers can provide the public with information about their clinical trials by using the Clinical Trials Listing Serviceprovided through CenterWatch, or look up more specific information on medicines and equipment using Drug and Device Pipeline News. Overall, the mission of CenterWatch is to be the leading source of news, directories, analysis, and proprietary market research for clinical research professionals and patients. It is located in Boston, MA. :NIF thanks the :Parkinson's Disease Foundation : :for their referral of this resource to us.

Proper citation: CenterWatch (RRID:SCR_001158) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.14/bioc/html/CGHbase.html

Software package that contains functions and classes that are needed by arrayCGH packages.

Proper citation: CGHbase (RRID:SCR_001279) Copy   

•   Source: SciCrunch Registry