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http://sourceforge.net/projects/blox/

A quantitative medical imaging and visualization program for use on brain MR, DTI, and MRS data. Programming Language: Java, JavaScript, Scheme

Proper citation: Blox (RRID:SCR_006667) Copy   

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https://precisionbiosystems.com/

An Antibody supplier

Proper citation: Precision Biosystems (RRID:SCR_006789) Copy   

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https://www.yonsei.ac.kr/en_sc/index.jsp

Private research university in Seoul, South Korea. Particularly respected in studies of medicine and business administration.

Proper citation: Yonsei University; Seoul; South Korea (RRID:SCR_006669) Copy   

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http://bionerds.sourceforge.net/

A named entity recognizer for the recovery of bioinformatics databases and software from primary literature. The entity recognizer achieved an F-measure of between 63% and 91% on different datasets (63%78% at the document level). Results from full-text literature analysis for both Genome Biology and BMC Bioinformatics journals are available as well as a full list of references and links for the various major resources mentioned. Data generated data can be used for exploration of bioinformatics database and software usage. This tool makes heavy use of GATE (version 6.1). It can be run in sandbox mode, which means a installation of GATE is not a prerequisite, but you will instead need to point the config to a unzipped gate_plugins directory instead (located in the bin/BMC_Files directory).

Proper citation: bioNerDS (RRID:SCR_006784) Copy   

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http://www.webgestalt.org/

Web based gene set analysis toolkit designed for functional genomic, proteomic, and large-scale genetic studies from which large number of gene lists (e.g. differentially expressed gene sets, co-expressed gene sets etc) are continuously generated. WebGestalt incorporates information from different public resources and provides a way for biologists to make sense out of gene lists. This version of WebGestalt supports eight organisms, including human, mouse, rat, worm, fly, yeast, dog, and zebrafish.

Proper citation: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit (RRID:SCR_006786) Copy   

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http://sourceforge.net/projects/virmid/

A Java based variant caller designed for disease-control matched samples. Virmid is also specialized for identifying potential within individual contamination where the disease sample cannot be purified enough. While the SNP calling rate is severely compromised with this heterogeneity, Virmid can uncover SNPs with low allele frequency by considering the level of contamination (alpha). The important features of Virmid are: * Estimation of accurate proporation of control sample in a (mixed) disease sample * Improved SNP and somatic mutation calling with regard to the estimated proportion

Proper citation: Virmid (RRID:SCR_006780) Copy   

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http://www.brainvoyager.com

Brain Innovation B.V. is developing scientific software in the field of human and animal brain imaging, neural network simulation and computer-based experimental control. Our current major product, BrainVoyager QX, is a commercially available cross-platform neuroimaging tool, which is used in hundreds of labs across the planet. Turbo-BrainVoyager is an easy to use program for real-time data analysis, which allows to observe a subject''s or patient''s brain activity during an ongoing functional MRI scanning session. TMS Neuronavigator provides the hard- and software to navigate a TMS coil to desired anatomical or functionally defined brain regions. We also provide free software products. BrainVoyager Brain Tutor allows to learn about brain areas by clicking on rotatable 3D brain models. StimulDX is a powerful stimulation software based on Microsofts DirectX API, which we will make available for free download in the near future.

Proper citation: Brain Innovation: Home of the BrainVoyager Product Family (RRID:SCR_006660) Copy   

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http://sourceforge.net/projects/bigpre/

A quality assessment software package for next-genomics sequencing data.

Proper citation: BIGpre (RRID:SCR_006781) Copy   

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http://www.pitt.edu/

Public research university in Pittsburgh, Pennsylvania. Pitt was founded by Hugh Henry Brackenridge in 1787 as the Pittsburgh Academy.

Proper citation: University of Pittsburgh; Pennsylvania; USA (RRID:SCR_006659) Copy   

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http://www.cdc.gov/osels/lspppo/Genetic_Testing_Quality_Practices/Nex-StoCT.html

National workgroup to define platform-independent approaches for establishing technical process elements of a quality management system (QMS) to assure the analytical validity and compliance of next-generation sequencing (NGS) tests with existing regulatory and professional quality standards. The workgroup identified and addressed gaps in quality practices that could compromise the quality of both clinical laboratory services and translational efforts needed to advance the implementation and utility of NGS in clinical settings. The workgroup was composed of experts with knowledge of and experience with NGS and included clinical laboratory directors, clinicians, platform and software developers and informaticians, as well as individuals actively engaged in NGS guideline development from accreditation bodies and professional organizations. Representatives from US government agencies also participated. These guidelines address four topics that are components of quality management in a clinical environment: (i) test validation, (ii) quality control (QC) procedures to assure and maintain accurate test results, (iii) the independent assessment of test performance through proficiency testing (PT) or alternative approaches and (iv) reference materials (RMs). Discussions were limited to the analytic and informatics processes required for accurate variant calling. The workgroup did not address how variants are prioritized, interpreted or reported.

Proper citation: Nex-StoCT (RRID:SCR_006777) Copy   

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http://purl.bioontology.org/ontology/BCGO

Ontology that assigns a grade to a tumor starting from the 3 criteria of the NGS

Proper citation: Breast Cancer Grading Ontology (RRID:SCR_006658) Copy   

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http://sammeth.net/confluence/display/FLUX/Home

Software to recontruct abundances of known transcript forms from RNAseq data. The algorithm works by distributing the reads mapping to a given exonic region (or splice junction) among the transcripts including the exon (or splice junction). The input is the annotation of a reference transcriptome and reads from RNAseq technologies aligned to the genome. From the reference annotation, splicing graphs are produced and reads are mapped to corresponding edges in these graphs according to the position where they align in the genomic sequence. The resulting graph with edges labelled by the number of reads can be interpreted as a flow network where each transcript representing a transportation path from its start to its end and consequently each edge a possibly shared segment of transportation along which a certain number of reads per nucleotide -- i.e., a flux -- is observed. Given a density function of reads along a transcript, the expected participation of each transcript in an edge under consideration can be estimated. The basic idea is to cast back from these latter participations and the observed number of reads - allowing for a certain amount of noise - to the original transcript abundancies. To do so, a linear constraint is formalized for each edge, and an optimal solution for the complete set of constraints is found by a standard linear program solver.

Proper citation: FLUX CAPACITOR (RRID:SCR_006651) Copy   

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http://www.nitrc.org/projects/randomwalks/

A simple interface to simulate Brownian motion in arbitrary, complex environments. The analysis routines enable visualization of these models with DTI, q-space, and higher order diffusion weighted MRI.

Proper citation: DW-MRI Random Walk Simulator (RRID:SCR_006652) Copy   

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http://www.emcdda.europa.eu/html.cfm/index190EN.html

The European Monitoring Centre for Drugs and Drug Addiction (EMCDDA) is the central source of comprehensive information on drugs and drug addiction in Europe. It was set up to provide factual, objective, reliable and comparable information concerning drugs, drug addiction and their consequences. Mission and work programme Just over a decade ago, Europes capacity for monitoring its drug problem was extremely limited. National approaches to the topic varied greatly and there was a lack of reliable and comparable information at European level concerning drugs, drug addiction and their consequences. In other words, it was impossible to talk with confidence about patterns and trends in drug use across the EU. The European Monitoring Centre for Drugs and Drug Addiction (EMCDDA) was founded in 1993 to change that. Inaugurated in Lisbon in 1995, the EMCDDA is the hub of drug-related information in the European Union. It exists to provide the EU and its Member States with a factual overview of European drug problems and a common information framework to support the drugs debate. The EMCDDA consists of a 90-strong team of specialists representing some 20 nationalities. Today it offers policy-makers the scientific evidence base they need for drawing up drug laws and strategies and helps professionals and researchers pinpoint best practice and new areas for analysis. Improving the comparability of drug information in the EU is central to the agencys work. To achieve this, the EMCDDA coordinates and relies on a network of some 30 national monitoring centres (Reitox network) to gather and analyse country data according to common data-collection standards and tools. The results of this national monitoring process are fed to the Lisbon centre for analysis and are ultimately released in the Annual report on the state of the drugs problem in Europe one of its many outputs. The EMCDDA has many working partners in Portugal. These include technical bodies primarily the Instituto da droga e da toxicodependncia which furnish the agency with the Portuguese drugs picture, and political bodies which use EMCDDA information when taking decisions on drug-related issues. In addition to cooperating with partners at national level, the EMCDDA also collaborates with its peers worldwide, having signed agreements with European and international organisations working in the drugs field. Over time, the EMCDDA has become not only Europes central reference point on drugs but also a respected authority globally. This interest has been reflected in visits by Heads of State and high-ranking politicians from all world regions and in requests from several non-EU countries for cooperation, whether in the area of technical assistance or the exchange of data and expertise. While the EMCDDA monitors the drug situation today, it is ever vigilant for new drugs and emerging trends that may pose a threat to Europes citizens tomorrow. With the production of cocaine and heroin at historically high levels and with around 7,000 Europeans dying every year of drug overdoses, constant monitoring is imperative. Public access to documents Citizens of the European Union and natural or legal persons residing or having their registered office in a Member State have the right of access to EMCDDA documents under Article 255(1) of the EC Treaty and Article 2(1) of Regulation (EC) No 1049/2001 in accordance with detailed rules laid out in the implementing rules adopted by the Management Board on 24 February 2006. This right to access concerns documents held by the EMCDDA, that is to say, documents drawn up or received by it and in its possession. Pursuant to article 2(2) of Regulation (EC) No 1049/2001, citizens of third countries not residing in a Member State and legal persons not having their registered office in one of the Member States shall enjoy the right of access to EMCDDA documents on the same terms as the beneficiaries referred to in Article 255(1) of the EC Treaty and Article 2(1) of Regulation (EC) No 1049/2001. All applications for access to a document should be sent by mail, fax or email, clearly stating the reference Application for access to EMCDDA documents. Funding The EMCDDA receives stable funding under Commission budget line B3-441 of the general budget of the European Union. Each year, a preliminary draft budget is presented by the Centre''s Director to the Management Board which may modify the draft before adopting it and submitting it to the European Commission. On this basis, the Commission presents its proposal for the annual funding to the EMCDDAs budget, to be adopted by the European Parliament and the Council. The implementation of the EMCDDA budget is subject to the external audit of the European Court of Auditors. The political responsibility for the execution of the budget rests with the EMCDDA''s Management Board, which adopts its own internal financial rules, based on the financial regulation applicable to the general budget of the European Communities.

Proper citation: European Monitoring Centre for Drugs and Drug Addiction (RRID:SCR_006654) Copy   

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https://github.com/nariai/tigar

Software to estimate transcript isoform abundances from RNA-Seq data by variational Bayesian inference. The statistical method can handle gapped alignments of reads against reference sequences so that it allows insertion or deletion errors within reads.

Proper citation: TIGAR (RRID:SCR_006650) Copy   

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http://compbio.bccrc.ca/software/apolloh/

A hidden Markov model (HMM) for predicting somatic loss of heterozygosity and allelic imbalance in whole tumour genome sequencing data.

Proper citation: APOLLOH (RRID:SCR_006648) Copy   

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http://www.abta.org/

Founded in 1973, the American Brain Tumor Association (ABTA) was the first national nonprofit organization dedicated solely to brain tumors. For nearly 40 years, the Chicago-based ABTA has provided critical funding to researchers working toward breakthroughs in brain tumor diagnosis, treatment and care, and is the only national organization providing comprehensive resources and serving the complex supportive care needs of brain tumor patients and caregivers from diagnosis through treatment and beyond.

Proper citation: American Brain Tumor Association (RRID:SCR_006649) Copy   

•   Source: SciCrunch Registry
  

https://www.phenx.org/Default.aspx?tabid=56

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on 05 01 2025. PhenX is a project to prioritize Phenotype and eXposure measures for Genome-wide Association Studies (GWAS). Leaders of the scientific community will assess and prioritize a broad range of domains relevant to genomics research and public health. The PhenX Steering Committee (SC), chaired by Dr. Jonathan Haines, provides leadership in the selection of domains and domain experts. Members of the SC include outstanding scientists from the research community and liaisons from the Institutes and Centers of the National Institutes of Health. Consensus measures for GWAS will have a direct impact on biomedical research and ultimately on public health. During the course of this project, up to 20 research domains will be examined, with up to 15 measures being recommended for use in future GWAS and other large-scale genomic research efforts. The goal is to maximize the benefits of future research by having comparable measures so that studies can be integrated. Each selected domain will be reviewed by a Working Group (WG) of scientists who are experts in the research area. A systematic review of the literature will guide the WGs selection of up to 15 high priority measures with standardized approaches for measurement. Selection criteria for the measures include factors such as validity, reproducibility, cost, feasibility, and burden to both investigators and participants. The scientific community will be asked to provide input on proposed measures. Consensus development is a key component of the project.

Proper citation: Consensus Measures for Phenotype and Exposure (RRID:SCR_006688) Copy   

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http://www.endocrine.niddk.nih.gov/

Information dissemination service of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) providing information about endocrine and metabolic diseases in easy-to-understand language: online, in booklets and fact sheets, by email, and over the phone to patients, health professionals and the public. The NEMDIS provides the following informational products and services: * Response to inquiries about endocrine and metabolic diseases, ranging from information about available patient and professional education materials to referrals to patient support organizations. Assistance is available by phone (8:30 a.m. to 5 p.m. eastern time, M-F), fax, mail, and email. * Publications about endocrine and metabolic diseases, provided free of copyright, in varying reading levels. Available online or in hard copy. NEMDIS also sends publications to health fairs and community events. * Referrals to health professionals through the National Library of Medicine''''s MEDLINEplus, which includes a consumer-friendly listing of organizations to assist in the search for physicians and other health professionals.

Proper citation: National Endocrine and Metabolic Diseases Information Service (RRID:SCR_006681) Copy   

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https://madb.nci.nih.gov/

Microarray data management and analysis system for NCI / Center for Cancer Research scientists / collaborators. Data is secured and backed up on a regular basis, and investigators can authorize levels of access privileges to their projects, allowing data privacy while still enabling data sharing with collaborators.

Proper citation: mAdb (RRID:SCR_006677) Copy   

•   Source: SciCrunch Registry