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http://www.cbs.dtu.dk/services/NetMHCpan/

Web server for quantitative prediction of peptide binding to any MHC molecule of known sequence using artificial neural networks. Characterizes binding specificity of given major histocompatibility complex molecule and predicts peptide length profile and peptide binding affinity. NetMHCpan 3.0 is improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length data sets. NetMHCpan 4.0 is trained on naturally eluted ligands and on peptide binding affinity data. NetMHCpan-4.1 server predicts binding of peptides to any MHC molecule of known sequence using artificial neural networks (ANNs).

Proper citation: NetMHCpan Server (RRID:SCR_018182) Copy   

•   Source: SciCrunch Registry

https://github.com/nci/drishti

Open source scientific visualisation software. Multi platform, volume exploration and presentation software. Used for visualising volumetric data, such as tomography data, electron microscopy data, etc.

Proper citation: Drishti (RRID:SCR_017999) Copy   

•   Source: SciCrunch Registry

https://github.com/ABCD-STUDY/auto-scoring

Visualization software that calculates derived scores for the electronic record system REDCap (Research Electronic Data Capture) to build and manage online surveys and databases. Used in the ABCD-STUDY (Adolescent Brain Cognitive Development - STUDY) report framework.

Proper citation: auto-scoring (RRID:SCR_016015) Copy   

•   Source: SciCrunch Registry

https://github.com/ABCD-STUDY/redcap-completion

Software to measure item level completion in a large REDCap project. It provides a web-interface to review data and it is used in the ABCD project to assess data collection sites for the reached level of completion.

Proper citation: redcap-completion (RRID:SCR_016019) Copy   

•   Source: SciCrunch Registry

https://web.archive.org/web/20180212152753/http://www.frantz.fi/software/gdpc.php

Software application for visualizing output data from molecular dynamics simulations. It can be customized to read almost any input file format, animate it, and output images of each frame.

Proper citation: gdpc (RRID:SCR_016119) Copy   

•   Source: SciCrunch Registry

http://phonbank.talkbank.org/

Database for study of early phonological development using Phon program. Child phonology component of TalkBank system.

Proper citation: PhonBank (RRID:SCR_016312) Copy   

•   Source: SciCrunch Registry

https://www.nichd.nih.gov/research/supported/NCS/researchers

Data and sample repository for National Children's Study. Provides access to data and samples collected from over 5,600 U.S. birth families to study environmental influences on child health and development. Data and biological and environmental samples are freely available, with approved request, for scientific research.

Proper citation: National Children's Study (NCS) Archive (RRID:SCR_016311) Copy   

•   Source: SciCrunch Registry

https://github.com/kingufl/cOMet

Software for error correction of optical mapping data.

Proper citation: cOMet (RRID:SCR_016276) Copy   

•   Source: SciCrunch Registry

https://biosyntax.org/

Software for syntax highlighting for computational biology.

Proper citation: bioSyntax (RRID:SCR_016207) Copy   

•   Source: SciCrunch Registry

http://www.eulerdiagrams.org/eulerAPE/

Software that uses ellipses to automatically draw accurate area-proportional Venn diagrams for 3-set data. It generates an exact diagram for most of the cases, and when it fails, the best diagram obtained through the hill climbing search is displayed, together with the inaccuracy values for each region.

Proper citation: eulerAPE (RRID:SCR_016457) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/RColorBrewer/index.html

Software tool to provide color schemes for maps and other graphics. R package to create colorful graphs with pre-made color palettes that visualize data.

Proper citation: RColorBrewer (RRID:SCR_016697) Copy   

•   Source: SciCrunch Registry

http://cistrome.org

Web based integrative platform for transcriptional regulation studies.

Proper citation: Cistrome (RRID:SCR_000242) Copy   

•   Source: SciCrunch Registry

http://www.africacentre.ac.za/Biobank/tabid/460/Default.aspx

THIS RESOURCE IS NO LONGER IN SERVICE, documented November 30, 2015. Extensive collection of biological specimens of various kinds that are mostly collected from the population around the Africa Centre in northern KwaZulu-Natal, but there are also specimens collected from populations in and around Durban and elsewhere in KwaZulu-Natal. The results of tests carried out on these specimens are generally stored in the main databases of the various studies involved, and are linkable back to the demographic and other data collected from the individuals concerned. The Biobank is curated by staff of the Africa Centre's Virology Laboratory in Durban, where all the specimens are currently stored, mostly in -80C freezers. A particular strength of its holdings are the dried blood spot (DBS), specimens five drops of blood on a filter-paper card, obtained via a finger-prick - of which there are now nearly 115,000. The following is a list of its holdings (May 2011): * 67,700 DBS specimens collected since late 2002 primarily for HIV prevalence estimation of the population covered by the Africa Centre Demographic Surveillance population. All have at least been tested for HIV, and just over 21% give a Positive result. Specimens are collected annually, so for some individuals we might have a sequence of 8-10 specimens covering 2002-2011. * 36,601 DBS specimens collected by the Vertical Transmission Study (VTS) between Sep 2001 and Dec 2006. This study focussed on mother-child pairs and investigated the vertical transmission of HIV from mother to child. DBS specimens were collected from both the mothers (at initial screening, and then from their children at Birth, 6, 10, 14, 18, 22 weeks, and 7, 8, 9, 12, 15, 18, 21 and 24 months. * 6,585 DBS specimens collected as part of the KZN IMPACT study of PMTCT effectiveness in six districts of kwaZulu-Natal. The specimens were collected during 2004-2006 from infants aged 4-8 weeks when mothers brought them to clinics for immunisation. These DBS specimens are stored at room temperature, not in freezers. * 3,524 DBS specimens collected as part of the Kesho Bora study from Sep 2007 . They were collected from mothers at enrollment, and from the infants at delivery, 2 weeks, and at 4, 5, 7, 8 and 15 months. * 50,068 Plasma specimens * 28,775 breastmilk specimens * 11,277 breastmilk products (Pellets and lactoserum). These have all been extracted from the BM specimens in prev. item? * 11,188 RNA and DNA products extracted from DBS and plasma specimens from all our major studies. * 5,735 Serum specimens * 3,505 cell pellets * 1,778 whole blood specimens * 1,284 Peripheral Blood Mononuclear Cells from the Kesho Bora study mothers (665) and their children (619) * 179 skin tissue specimens from the KST study (Kaposi's Sarcoma) * 176 foreskins

Proper citation: Africa Centre Biobank (RRID:SCR_000638) Copy   

•   Source: SciCrunch Registry

http://neuromorphometrics.org:8080/nvm/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6, 2023. Software tool for quantitative neuroanatomical measurements in volumetric image data. Used to draw regions of interest for subsequent fMRI analysis.

Proper citation: NVM (RRID:SCR_000600) Copy   

•   Source: SciCrunch Registry

http://www.pd-doc.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on December 02, 2011. Notice: This domain name expired on 10/29/11 and is pending renewal or deletion PD-DOC is a portal and a database resource, hosting a database and linking to other databases and data sets of clinical and translational data. PD-DOC functions to organize and facilitate clinical and translational research in Parkinson's disease. The PD-DOC Database contains standardized data collected by user institutions on large numbers of patients with Parkinsons disease and other parkinsonian disorders. In some cases, data is obtained at a single point in time, while in others data is collected repeatedly over time. The PD-DOC Database is composed of the Core Data Set (CDS) which consists of those variables required to be gathered for each subject whose data is entered into the PD-DOC database. In 2005, working groups of Udall Center and invited experts deliberated to establish the components of each CDS section (e.g. General Clinical, Cognitive/Behavioral, Postmortem Brain Neuropathological Findings). The PD-DOC CDS was established and designed to optimize data analyses and data mining for large numbers of subjects participating in a variety of research studies. In most cases corresponding DNA samples are available form the NINDS Human Genetic Repository (at Coriell). Much of the website is publicly available for viewing. To request access to sections of the website dealing with downloading or requesting data, requesting a consultation, or submitting data or other information you will need to register. Before registering, you should read the PD-DOC Policies. Note that PD-DOC data can be used for research purposes only. Once your registration is successfully completed you will be automatically logged into the website.

Proper citation: PD-DOC (RRID:SCR_001596) Copy   

•   Source: SciCrunch Registry

https://github.com/ElementoLab/ChIPseeqer

Software that provides a comprehensive framework for the analysis of ChIP-seq data.

Proper citation: ChIPseeqer (RRID:SCR_001545) Copy   

•   Source: SciCrunch Registry

http://mobile.ebiocenter.com/ebionews/

eBioNews specializes in online information services and resource exchanges in the fields of life sciences and biotechnology. By applying its knowledge database and content management system (CMS), eBioNews offers readers and customers the organized and comprehensive information. eBioNews also provides a membership-based service to assist our customers in information and data search, processing, storage, and sharing. Generally, eBioNews covers the following areas: - life science frontiers - news and discussions - features and specials - resources and sourcing - career development - academic and industry - training and education Additionally, eBioNews information is organized into the following two clusters: - News Center: 1. Headlights 2. Research Frontiers 3. General Research 4. Clinical Development 5. Enterprise & Industry 6. Products & Services 7. Investment & Financials 8. Features 9. Newsletter The News Center consists of the elements and mechanisms that enable collecting, organizing, displaying, and delivering life science related information, data, and knowledge. - Resource Center: 1. eBioResources 2. Cooperation 3. Events 4. Human Resources 5. Intellectual Property 6. Finance & Legal 7. Operations 8. Organization 9. Publication The Resource Center is a system that hosts and facilitates the resource-related information between and among multiple parties, especially for promoting cooperation, collaboration, consortium, partnering, joint venture, licensing, out-sourcing, and trading. Sponsors: This resource is supported by eBioCenter Corporation.

Proper citation: eBioNews - A Subsidiary of eBioCenter (RRID:SCR_001717) Copy   

•   Source: SciCrunch Registry

http://neuroimage.usc.edu/brainstorm/

Software as collaborative, open source application dedicated to analysis of brain recordings: MEG, EEG, fNIRS, ECoG, depth electrodes and animal invasive neurophysiology. User-Friendly Application for MEG/EEG Analysis.

Proper citation: Brainstorm (RRID:SCR_001761) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/itk-snap/

Open source interactive software application for three dimentional medical images, manual delineation of anatomical regions of interest, and performing automatic image segmentation. Used for delineating anatomical structures and regions in MRI, CT and other 3D biomedical imaging data.WebGL-based viewer for volumetric data. It is capable of displaying arbitrary (non axis-aligned) cross-sectional views of volumetric data, as well as 3-D meshes and line-segment based models (skeletons).

Proper citation: ITK-SNAP (RRID:SCR_002010) Copy   

•   Source: SciCrunch Registry

https://datashare.nida.nih.gov

Website which allows data from completed clinical trials to be distributed to investigators and public. Researchers can download de-identified data from completed NIDA clinical trial studies to conduct analyses that improve quality of drug abuse treatment. Incorporates data from Division of Therapeutics and Medical Consequences and Center for Clinical Trials Network.

Proper citation: NIDA Data Share (RRID:SCR_002002) Copy   

•   Source: SciCrunch Registry