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http://www.biausa.org/

The country''s oldest and largest nationwide brain injury advocacy organization. We are dedicated to increasing access to quality health care and raising awareness and understanding of brain injury through advocacy, education and research. With a nationwide network of more than 40 chartered state affiliates and hundreds of local chapters and support groups, we provide help, hope and healing for individuals who live with brain injury, their families and the professionals who serve them. Brain injury is not an event or an outcome. It is the start of a misdiagnosed, misunderstood, under-funded neurological disease. Individuals who sustain brain injuries must have timely access to expert trauma care, specialized rehabilitation, lifelong disease management and individualized services and supports in order to live healthy, independent and satisfying lives.

Proper citation: Brain Injury Association of America (RRID:SCR_006639) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/powermap/

Software tool specifically designed for neuroimaging data that implements theoretical power calculation algorithms based on non-central random field theory. It can also calculate power for statistical analyses with FDR (false discovery rate) corrections. This GUI (graphical user interface)-based tool enables neuroimaging researchers without advanced knowledge in imaging statistics to calculate power and sample size in the form of 3D images. This tool is currently under limited release for beta testing. At this time, only users that have been directed to this site by the PowerMap developers will receive support.

Proper citation: PowerMap (RRID:SCR_006721) Copy   

•   Source: SciCrunch Registry

http://www.proteinatlas.org/

Open access resource for human proteins. Used to search for specific genes or proteins or explore different resources, each focusing on particular aspect of the genome-wide analysis of the human proteins: Tissue, Brain, Single Cell, Subcellular, Cancer, Blood, Cell line, Structure and Interaction. Swedish-based program to map all human proteins in cells, tissues, and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics, and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome.

Proper citation: The Human Protein Atlas (RRID:SCR_006710) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/dmeas/

A user-friendly DNA methylation analysis tool for DNA methylation pattern extraction, DNA methylation level estimation, DNA methylation entropy analysis and multi-sample comparison. It was developed in order to assess the DNA methylation variations for a given genomic locus or genome-wide methylation data.

Proper citation: DMEAS (RRID:SCR_006679) Copy   

•   Source: SciCrunch Registry

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

An R package for deconvolution of heterogeneous tissues based on mRNA-Seq data. It modeled expression levels from heterogeneous cell populations in mRNA-Seq as the weighted average of expression from different constituting cell types and predicted cell type proportions of single expression profiles.

Proper citation: DeconRNASeq (RRID:SCR_006713) Copy   

•   Source: SciCrunch Registry

http://www.upr.edu/

Main public university system in the U.S. Commonwealth of Puerto Rico and a government-owned corporation.The oldest and largest higher learning institution in the Caribbean.

Proper citation: University of Puerto Rico; Puerto Rico; USA (RRID:SCR_006707) Copy   

•   Source: SciCrunch Registry

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

Software package that allows the visualization of DNA methylation data after bisulfite sequencing.

Proper citation: methVisual (RRID:SCR_006705) Copy   

•   Source: SciCrunch Registry

https://www.oxfordbiomed.com/

An Antibody supplier

Proper citation: Oxford Biomedical Research (RRID:SCR_006864) Copy   

•   Source: SciCrunch Registry

http://www.niehs.nih.gov/research/resources/software/biostatistics/eagleview/

An information-rich viewer for next-generation genome assembles with data integration capability. EagleView can display a dozen different types of information including base qualities, machine specific trace signals, and genome feature annotations. It provides an easy way for inspecting visually the quality of a genome assembly and validating polymorphism candidate sites (e.g., SNPs) reported by polymorphism discovery tools. It can also facilitate data interpretation and hypothesis generation. EagleView is a multi-platform application developed with C++ and is available for all three major platforms: Windows, Linux, and Mac OS.

Proper citation: EagleView (RRID:SCR_006859) Copy   

•   Source: SciCrunch Registry

http://csbio-linux001.cs.unc.edu/nextgen/software/FDM/

A graph-based statistical method to detect differential transcription using RNA-seq data.

Proper citation: FDM (RRID:SCR_006733) Copy   

•   Source: SciCrunch Registry

http://www.hematology.org/

The American Society of Hematology (ASH) is the world''s largest professional society concerned with the causes and treatments of blood disorders. The mission of the Society is to further the understanding, diagnosis, treatment, and prevention of disorders affecting the blood, bone marrow, and the immunologic, hemostatic and vascular systems, by promoting research, clinical care, education, training, and advocacy in hematology.

Proper citation: American Society of Hematology (RRID:SCR_006734) Copy   

•   Source: SciCrunch Registry

https://simonsfoundation.org/

The Simons Foundation is a private foundation based in New York City, incorporated in 1994 by Jim and Marilyn Simons. The Simons Foundation''s mission is to advance the frontiers of research in mathematics and the basic sciences. We sponsor a range of programs that aim to promote a deeper understanding of our world. The primary focus of the foundation''s Mathematics & the Physical Sciences (MPS) program is on the theoretical sciences radiating from mathematics: in particular, the fields of mathematics, theoretical computer science and theoretical physics. Although we have supported basic research in mathematics and physics for years at institutions around the globe, the mode of our support entered an important new phase in fall 2009 with the introduction of grant opportunities with open application procedures. It is intended that this will become our primary mode of operation. In 2010, the MPS program issued its first requests for grant applications. These requests offered grants to establish post-doctoral fellowships, grants to promote collaboration between researchers, grants to create professorships that combine mathematics with other fields, and a grant to endow an institute for theoretical computer science. Other projects are under way, including the Africa Mathematics Project, intended to bolster mathematics scholarship on the African continent, and an oral history project: a series of interviews with renowned mathematicians and scientists which will be made available to the public for viewing. The Simons Foundation''s initial support of life sciences work has tended to focus on research that promotes synergy between biology and mathematics. Such projects have included quantitative biology programs at Cold Spring Harbor Laboratory, the Institut des Hautes ��tudes Scientifiques, the Institute for Advanced Study, and The Rockefeller University. The Life Sciences program is expected to expand in scope over the next two to three years. To date, the Simons Foundation''s single largest initiative has been in autism research. The Simons Foundation Autism Research Initiative (SFARI) program seeks to improve the diagnosis and treatment of autism spectrum disorders by funding, catalyzing, and driving innovative research of the greatest quality and relevance. In 2007, SFARI issued its first Request for Applications, its goal being to attract the best researchers to the field. In the years since, SFARI has given grants to 150 investigators in the United States and abroad. Additionally, to facilitate the field as a whole, SFARI has created the Simons Simplex Collection of extensive genetic and phenotypic data from almost 3,000 families with a child affected by autism. Although SFARI''s immediate priority is to benefit individuals challenged by autism spectrum disorders, the program''s research is expected to yield insights into the neural mechanisms of fundamental human capabilities, complementing the mission of the Simons Foundation to advance research in the basic sciences and mathematics.

Proper citation: Simons Foundation (RRID:SCR_006735) Copy   

•   Source: SciCrunch Registry