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Medical school of the University of Pennsylvania. It is located in the University City section of Philadelphia.
Proper citation: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA (RRID:SCR_013302) Copy
http://www.jisc.ac.uk/whatwedo/programmes/mrd/clip/webtracks.aspx
This project will develop an approach and mechanism to address the construction and propagation of linked data in the context of research and academic endeavour. The proposed work will build experiments in previous projects (Claddier, StoreLink) to develop a peer-to-peer protocol to underpin the construction of a web of linked data. This set of semantically annotated links between data resources forms a graph of citation and provenance and the project will build value added services to exploit these features. The project will address the following specific objectives: * To specify and implement the Intercom Protocol so that it can communicate a range of types of semantic links between resources via a secure communication mechanism. * To develop a practical working scenario involving data repositories, publication repositories, open science notebooks and publishers. * To develop aggregation techniques supporting added value services in search and impact analysis. * To evaluate of the approach with the identified stakeholders groups.
Proper citation: Webtracks (RRID:SCR_006615) Copy
http://bioconductor.org/packages/release/bioc/html/casper.html
Software to infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start distributions non-parametrically, which improves estimation precision.
Proper citation: casper (RRID:SCR_006613) Copy
Collaborative venture between the National Institute of Mental Health (NIMH) and several academic institutions. Repository facilitates psychiatric genetic research by providing patient and control samples and phenotypic data for wide-range of mental disorders and Stem Cells.Stores biosamples, genetic, pedigree and clinical data collected in designated NIMH-funded human subject studies. RGR database likewise links to other repositories holding data from same subjects, including dbGAP, GEO and NDAR. Allows to access these data and biospecimens (e.g., lymphoblastoid cell lines, induced pluripotent cell lines, fibroblasts) and further expand genetic and molecular characterization of patient populations with severe mental illness.
Proper citation: NIMH Repository and Genomics Resources (RRID:SCR_006698) Copy
Antibody and density gradient media supplier.
Proper citation: Progen (RRID:SCR_006726) Copy
http://rulai.cshl.edu/splicetrap/
A statistic tool for quantifying exon inclusion ratios in paired-end RNA-seq data, with broad applications for the study of alternative splicing. SpliceTrap approaches to exon inclusion level estimation as a Bayesian inference problem. For every exon it quantifies the extent to which it is included, skipped or subjected to size variations due to alternative 3?/5? splice sites or Intron Retention. In addition, SpliceTrap can quantify alternative splicing within a single cellular condition, with no need of a background set of reads.
Proper citation: SpliceTrap (RRID:SCR_006728) Copy
https://github.com/arq5x/bedtools2
A powerful toolset for genome arithmetic allowing one to address common genomics tasks such as finding feature overlaps and computing coverage. Bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.
Proper citation: BEDTools (RRID:SCR_006646) Copy
The Down Syndrome Research and Treatment Foundation is dedicated to finding a treatment to improve cognition including learning, memory and speech for individuals with Down syndrome. Since our founding in 2004 we have become the leading private source of funding in the United States for Down syndrome cognition research. The mission of DSRTF is to stimulate biomedical research that will accelerate the development of treatments to significantly improve cognition, including memory, learning and speech, for individuals with Down syndrome in order that they: * participate more successfully in school; * lead more active and independent lives; * and avoid the early onset of Alzheimer''s Disease. DSRTF is funding research that applies the information, tools and techniques resulting from the genome project along with recent advances in brain research to the study of cognition in Down syndrome. Our goal is the development of treatments that will improve learning, memory, and speech, and therefore enhance the lives of those with Down syndrome and their families. The majority of individuals with Down syndrome fall into the mild to moderate range of cognitive impairment. For many of these individuals, a 10%-20% improvement in cognitive ability would provide them with the ability to live independently, hold a job and be fully integrated within their communities.
Proper citation: Down Syndrome Research and Treatment Foundation (RRID:SCR_006637) Copy
http://sourceforge.net/projects/niftysim/
A high-performance nonlinear finite element solver. A key feature is the option of GPU-based execution, which allows the solver to significantly out-perform equivalent commercial packages.
Proper citation: NiftySim (RRID:SCR_006591) Copy
https://wiki.nci.nih.gov/display/LexEVS/LexGrid
LexGrid (Lexical Grid) provides support for a distributed network of lexical resources such as terminologies and ontologies via standards-based tools, storage formats, and access/update mechanisms. The Lexical Grid Vision is for a distributed network of terminological resources. It is the foundation of the National Center for Biomedical Ontology BioPortal interface and web-services, and can parse OBO format, as well as other formats such as OWL. Currently, there are many terminologies and ontologies in existence. Just about every terminology has its own format, its own set of tools, and its own update mechanisms. The only thing that most of these pieces have in common with each other is their incompatibility. This makes it very hard to use these resources to their full potential. We have designed the Lexical Grid as a way to bridge terminologies and ontologies with a common set of tools, formats and update mechanisms. The Lexical Grid is: * accessible through a set of common APIs * joined through shared indices * online accessible * downloadable * loosely coupled * locally extendable * globally revised * available in web-space on web-time * cross-linked The realization of this vision requires three interlocking components, which are: * Standards - access methods and formats need to be published and openly available * Tools - standards based tools must be readily available * Content - commonly used terminologies have to be available for access and download Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Proper citation: LexGrid (RRID:SCR_006627) Copy
http://www.alexaplatform.org/alexa_seq/index.htm
A method for using massively parallel paired-end transcriptome sequencing for ''alternative expression analysis''.
Proper citation: ALEXA-Seq (RRID:SCR_006700) Copy
http://sourceforge.net/projects/splicegrapher/
Software that predicts alternative splicing patterns and produces splice graphs that capture in a single structure the ways a gene''s exons may be assembled. It enhances gene models using evidence from next-generation sequencing and EST alignments.
Proper citation: SpliceGrapher (RRID:SCR_006657) Copy
http://www.bioconductor.org/packages/devel/bioc/html/ChIPXpress.html
A R package designed to improve ChIP-seq and ChIP-chip target gene ranking using publicly available gene expression data. It takes as input predicted transcription factor (TF) bound genes from ChIPx data and uses a corresponding database of gene expression profiles downloaded from NCBI GEO to rank the TF bound targets in order of which gene is most likely to be functional TF target.
Proper citation: ChIPXpress (RRID:SCR_006653) Copy
http://www.nitrc.org/projects/webmill/
Web game that provides an innovative infrastructure for labeling to enable an alternative to expert raters for medical image labeling through statistical analysis of the collaborative efforts of many, minimally-trained raters. Statistical atlases of regional brain anatomy have proven to be extremely useful in characterizing the relationship between the structure and function of the human nervous system. Typically, an expert human rater manually examines each slice of a three-dimensional volume. This approach can be exceptionally time and resource intensive, so cost severely limits the clinical studies where subject-specific labeling is feasible. Methods for improved efficiency and reliability of manual labeling would be of immense benefit for clinical investigation into morphological correlates of brain function.
Proper citation: Web Game for Collaborative Labeling (RRID:SCR_006685) Copy
https://code.google.com/p/softsearch/
A sensitive structural variant (SV) detection software tool for Illumina paired-end next-generation sequencing data. It simultaneously utilizes soft-clipping and read-pair strategies for detecting SVs to increase sensitivity. Soft clips are proxies for split-reads that indicate part of the read maps to the reference genome, but the other part is not localized at the same place (e.g. breakpoint spanning reads). Discordant read-pairs refer to a read and its mate, where the insert size is greater (or less than) the expected distribution of the dataset ? or ? where the mapping orientation of the reads is unexpected (e.g. both on the same strand). SoftSearch looks for areas with soft-clipping in the genome that have discordant read pairs supporting the anomaly. Once areas with both these conditions are identified, the read and mate information is extracted directly from the BAM file containing the discordant reads, obviating the need for time-consuming and error-prone complex alignment strategies. Only a small number of soft-masked bases discordant read-pairs are necessary to identify an SV, which on their own would not be sufficient to make an SV call, thus highlighting SoftSearch?s improved sensitivity. SoftSearch is well suited to be ?plugged in? to most sequence analysis workflows, since it requires standard file inputs, such as a BAM file using almost any aligner and a reference genome FASTA file. Because SoftSearch requires soft-masked bases, the only requirement is that the aligner must have this functionality, which is usually turned on by default by many standard aligners (e.g. BWA, Novoalign, etc).
Proper citation: SoftSearch (RRID:SCR_006683) Copy
A semantically annotated corpus of 240 MEDLINE abstracts (167 on the subject of E. coli species and 73 on the subject of the Human species) intended for training information extraction (IE) systems and/or resources which are used to extract events from biomedical literature. The corpus has been manually annotated with events relating to gene regulation by biologists. Each event is centered on either a verb (e.g. transcribe) or nominalized verb (e.g. transcription) and annotation consists of identifying, as exhaustively as possible, the structurally-related arguments of the verb or nominalized verb within the same sentence. Each event argument is then assigned the following information: * A semantic role from a fixed set of 13 roles which are tailored to the biomedical domain. * A biomedical concept type (where appropriate). The corpus in available for download in 2 formats: * A standoff format, based on the BioNLP'09 Shared Task format * An XML format, based on the GENIA event annotation format
Proper citation: GREC Corpus (RRID:SCR_006719) Copy
Network of three teaching hospitals affiliated with the medical school of Université Laval and several specialized institutions in Quebec City.
Proper citation: University of Quebec Hospital Centre; Quebec; Canada (RRID:SCR_006740) Copy
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