Tools   Select Another Resource Report Type

http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/sspacev12/

A stand-alone software program for scaffolding pre-assembled contigs using paired-read data. Main features are: a short runtime, multiple library input of paired-end and/or mate pair datasets and possible contig extension with unmapped sequence reads.

Proper citation: SSPACE (RRID:SCR_005056) Copy   

•   Source: SciCrunch Registry

http://meringlab.org/software/hpc-clust/

A set of tools designed to cluster large numbers (>1 million) of pre-aligned nucleotide sequences. It performs the clustering of sequences using the Hierarchical Clustering Algorithm (HCA). There are currently three different cluster metrics implemented: single-linkage, complete-linkage, and average-linkage. In addition, there are currently four sequence distance functions implemented, these are: identity (gap-gap counting as match), nogap (gap-gap being ignored), nogap-single (like nogap, but consecutive gap-nogap''s count as a single mismatch), tamura (distance is calculated with the knowledge that transitions are more likely than transversions). One advantage that HCA has over other algorithms is that instead of producing only the clustering at a given threshold, it produces the set of merges occuring at each threshold. With this approach, the clusters can afterwards very quickly be reported for every arbitrary threshold with little extra computation. This approach also allows the plotting of the variation of number of clusters with clustering threshold without requiring the clustering to be run for each threshold independently. Another feature of the way HPC-CLUST is implemented is that the single-, complete-, and average-linkage clusterings can be computed in a single run with little overhead.

Proper citation: HPC-CLUST (RRID:SCR_005052) Copy   

•   Source: SciCrunch Registry

http://www.openphacts.org/

Project that developed an open access discovery platform, called Open Pharmacological Space (OPS), via a semantic web approach, integrating pharmacological data from a variety of information resources and tools and services to question this integrated data to support pharmacological research. The project is based upon the assimilation of data already stored as triples, in the form subject-predicate-object. The software and data are available for download and local installation, under an open source and open access model. Tools and services are provided to query and visualize this data, and a sustainability plan will be in place, continuing the operation of the Open PHACTS Discovery Platform after the project funding ends. Throughout the project, a series of recommendations will be developed in conjunction with the community, building on open standards, to ensure wide applicability of the approaches used for integration of data.

Proper citation: Open PHACTS (RRID:SCR_005050) Copy   

•   Source: SciCrunch Registry

http://www.vetmed.ucdavis.edu/cceh/

The Center for Children''s Environmental Health and Disease Prevention is a multi-disciplinary collaborative research organization established to examine how toxic chemicals may influence the development of autism in children. The Center''s goal is to contribute knowledge about autism that will lead to new strategies for the prevention and treatment of this mysterious condition. Parents and health professionals have raised concerns about how environmental factors such as pesticides, a variety of chemicals, or even some ingredients included in vaccines may effect the development of the disorder. We are the first center to examine the roles of a wide range of toxic chemicals, genetic predisposition, and the interplay between these two in altering brain development during early life and leading to abnormal social behavior in children. Scientists in the CCEH study the effects of the environment on children''s health, with a particular focus on autism. Researchers come from all fields including molecular biology, medicine, nutrition, psychology, animal behavior, and genetics. The Center''s research is guided by an Advisory Board with representatives including parents, activists, non-profits, government agencies, and concerned citizens. This Center is one of several children''s centers throughout the nation funded by the U.S. EPA and NIEHS.

Proper citation: UC Davis Center for Childrens Environmental Health (RRID:SCR_004998) Copy   

•   Source: SciCrunch Registry

http://bbmri-wiki.wikidot.com/start

The BBMRI Wiki is intended to help establish a standard vocabulary within the European BBMRI (Biobanking and Biomolecular Resources Research Infrastructure) project. This Wiki also facilitates the definition and updating of new terms as well as the Minimum Information About BIobank data Sharing: MIABIS. MIABIS represents the minimum information required to enable the exchange of biological samples and data between biobanks.

Proper citation: BBMRI Wiki (RRID:SCR_004994) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/popset

Database containing a set of DNA sequences that have been collected to analyse the evolutionary relatedness of a population. The population could originate from different members of the same species, or from organisms from different species. Users may submit a Popset using Sequin.

Proper citation: NCBI Popset (RRID:SCR_005049) Copy   

•   Source: SciCrunch Registry

http://plaza.ufl.edu/xywang/Mpick.htm

A modularity-based clustering software for Operational Taxonomic Unit (OTU) picking of 16S rRNA sequences. The algorithm does not require a predetermined cut-off level, and our simulation studies suggest that it is superior to existing methods that require specified distance or variance levels to define OTUs.

Proper citation: M-pick (RRID:SCR_004995) Copy   

•   Source: SciCrunch Registry

http://www.manchester.ac.uk/

Public research university in Manchester, England, formed in 2004 by merger of University of Manchester Institute of Science and Technology and Victoria University of Manchester. Second largest university in United Kingdom by enrollment.

Proper citation: University of Manchester; Manchester; United Kingdom (RRID:SCR_004996) Copy   

•   Source: SciCrunch Registry

https://bxcell.com/

Commercial supplier and developer of in vivo antibodies. Provides antibodies and antibody production services.

Proper citation: Bio X Cell (RRID:SCR_004997) Copy   

•   Source: SciCrunch Registry

http://plaza.ufl.edu/sunyijun/ES-Tree.htm

Software for hierarchical Clustering Analysis of Millions of 16S rRNA Pyrosequences in Quasi-linear Time.

Proper citation: ESPRIT-Tree (RRID:SCR_005045) Copy   

•   Source: SciCrunch Registry

http://english.hust.edu.cn/

Public research university located in Guanshan Subdistrict, Hongshan District, Wuhan, Hubei province, China.

Proper citation: Huazhong University of Science and Technology; Wuhan; China (RRID:SCR_005047) Copy   

•   Source: SciCrunch Registry

http://glioblastoma.alleninstitute.org/

Platform for exploring the anatomic and genetic basis of glioblastoma at the cellular and molecular levels that includes two interactive databases linked together by de-identified tumor specimen numbers to facilitate comparisons across data modalities: * The open public image database, here, providing in situ hybridization data mapping gene expression across the anatomic structures inherent in glioblastoma, as well as associated histological data suitable for neuropathological examination * A companion database (Ivy GAP Clinical and Genomic Database) offering detailed clinical, genomic, and expression array data sets that are designed to elucidate the pathways involved in glioblastoma development and progression. This database requires registration for access. The hope is that researchers all over the world will mine these data and identify trends, correlations, and interesting leads for further studies with significant translational and clinical outcomes. The Ivy Glioblastoma Atlas Project is a collaborative partnership between the Ben and Catherine Ivy Foundation, the Allen Institute for Brain Science and the Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment.

Proper citation: Ivy Glioblastoma Atlas Project (RRID:SCR_005044) Copy   

•   Source: SciCrunch Registry

http://druginfo.nlm.nih.gov/drugportal/drugportal.jsp

The NLM Drug Information Portal gives users a gateway to selected drug information from the U.S. National Library of Medicine and other key U.S. Government agencies. At the top of the page are links to individual resources with potential drug information, including summaries tailored to various audiences. Resources include the NLM search systems useful in searching for a drug, NLM research resources, resources organized by audience and class, and other NIH and government resources such as FDA and CDC. The search box in the middle of the page lets you search many of these resources simultaneously. More than 34,000 drugs can be searched using this facility. The portal covers drugs from the time they are entered into clinical trials (Clinicaltrials.gov) through their entry in the U.S. market place (Drugs@FDA). Many drugs in other countries are covered, but not as thoroughly as U.S. drugs. The PubMed link provides medical literature describing research, and TOXLINE provides toxicology literature. Resources such as MedlinePlus provide easy to read summaries of the uses and efficacy of a drug. You may search by a drug's trade name or generic name. For example, the trade name Advil and the generic name ibuprofen will retrieve the same drug record. As you type in a name, suggestions are given beneath the search box. A spell checker gives suggestions if the name is not found. You can find embedded portions of names by using an asterisk at the beginning and/or end of a search term. You can also search by the general Category of usage of a drug by checking that radio button. Suggestions are given as you type here too. Once a drug is found, a summary of the drug's type and usage is given, as well as links leading to further information at one of the portal's resources. Outside links open in a new window. Within a given drug record, you may click on the drug category and retrieve drugs with the same or similar uses. * View drug category descriptions. * View top By Name searches (previous seven days). * View top By Category searches (previous seven days). * View top dispensed prescriptions in the US Market, 2010. * View common drug name list. * View category name list. * View list of resources searched. JavaScript must be enabled in your browser for the NLM Drug Information Portal to work properly.

Proper citation: Drug Information Portal (RRID:SCR_002818) Copy   

•   Source: SciCrunch Registry

http://www.genomesonline.org/

Database of information regarding genome and metagenome sequencing projects, and their associated metadata, around the world. It also provides information related to organism properties such as phenotype, ecotype and disease. Both complete and ongoing projects, along with their associated metadata, can be accessed. Users can also register, annotate and publish genome and metagenome data.

Proper citation: Genomes Online Database (RRID:SCR_002817) Copy   

•   Source: SciCrunch Registry

http://www.geneontology.org/

Computable knowledge regarding functions of genes and gene products. GO resources include biomedical ontologies that cover molecular domains of all life forms as well as extensive compilations of gene product annotations to these ontologies that provide largely species-neutral, comprehensive statements about what gene products do. Used to standardize representation of gene and gene product attributes across species and databases.

Proper citation: Gene Ontology (RRID:SCR_002811) Copy   

•   Source: SciCrunch Registry

http://www.cuni.cz/UKEN-1.html

Research university located in Prague, Czech Republic.

Proper citation: Charles University; Prague; Czech Republic (RRID:SCR_002931) Copy   

•   Source: SciCrunch Registry

http://www.genox.com

Biotechnological company that produces and supplies materials to oxidative stress and aging researchers.

Proper citation: Genox Corpooration (RRID:SCR_002930) Copy   

•   Source: SciCrunch Registry

http://biohealth.snu.ac.kr/software/TRAP/

A comprehensive software package integrating all necessary tasks such as mapping short reads, measuring gene expression levels, finding differentially expressed genes (DEGs), clustering and pathway analysis for time-series data in a single environment.

Proper citation: Time-series RNA-seq Analysis Package (RRID:SCR_002935) Copy   

•   Source: SciCrunch Registry

http://www.cisreg.ca/

This portal leads to the numerous Wasserman Lab online software tools available for use. The following are list of active Software tools available: - ConSite: Transcription factor binding site detection using phylogenetic footprinting - dbMTN: Multiple Tissue Northern Blot Comparison Tool - Gene Set Builder: A tool for collation, curation and distribution of sets of genes - The Gene Characterization Index: a bioinformatics method for scoring the extent to which a protein-encoding gene is functionally described - JASPAR: Transcription Factor Binding Profile Database - MSCAN: Algorithm that detects clusters of transcription factor binding sites in genomic sequences - NHRscan: A computational predictor of nuclear hormone receptor binding sites - oPOSSUM: Web-based analysis of over-represented transcription factor binding sites - ORCA: Transcription factor binding site detection using phylogenetic footprinting (alternative to ConSite) - OrthoSeq: Alignment of DNA sequences - PAZAR: An open-access system for the collection and dissemination of regulatory sequence annotation - Phylofoot: Tools for phylogenetic footprinting - RAVEN: Regulatory analysis of Variation in ENhancers - SAGE2Splice: A tool that uses unmapped SAGE tags to predict novel splice junctions in the genome - TFBS: Perl modules for transcription factor binding site detection and analysis - TFCat: TFCat is a catalog of mouse and human TFs based on a reliable core collection of annotations obtained by expert review of the scientific literature. - TFe: An online encyclopedic collection of well-studied transcription factor proteins in the human, mouse, and rat genomes - Ulysses: Protein Interactions Conserved Across Evolution

Proper citation: Wasserman Lab Online Software Tools (RRID:SCR_002892) Copy   

•   Source: SciCrunch Registry

http://www.genscript.com

Commercial organization which provides life science services and products to researchers. They specialize in gene synthesis, peptide, protein, antibody and preclinical drug development service.

Proper citation: GenScript (RRID:SCR_002891) Copy   

•   Source: SciCrunch Registry