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http://compbio.cs.wayne.edu/software/squeezambler/
Software to sequence and de novo assemble all distinct genomes present in a microbial sample with a sequencing cost and computational complexity proportional to the number of genome types, rather than the number of cells.
Proper citation: Squeezambler (RRID:SCR_004385) Copy
http://www.childhoodbraintumor.org/
The Childhood Brain Tumor Foundation (CBTF), an all-volunteer organization, was founded in 1994 by families, friends and physicians of children with brain tumors. Our mission is to raise funds for scientific research and heighten public awareness of this most devastating disease and to improve prognosis and quality of life for those that are affected. Founded and incorporated in Virginia, relocated to Maryland in 1998, the Foundation (a 501(c) (3), strives to meet the goals of our mission. Friends, families, and physicians brought CBTF together and are dedicated to serving the needs of families and children with brain tumors, in hopes of improving the quality of life and find cures for pediatric brain tumors. Annually, CBTF funds basic science or clinical research for pediatric brain tumors; conferences and other programs. We provide informational materials on our website and mail other information (nationally and internationally) upon request. The Childhood Brain Tumor Foundation (CBTF) has funded state-of-the-art research and supported conferences for pediatric brain tumors over the past 17 years. Grants submissions are reviewed thoroughly by our dedicated renown team of scientific advisors to ensure that CBTF selects the highest quality research for pediatric brain tumors. Each year, we receive so many outstanding applications and it is through the support of private and public donations that this is all possible. With your support, together, we will strive to find a cure for children''s brain tumors.
Proper citation: Childhood Brain Tumor Foundation (RRID:SCR_004421) Copy
Improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays.
Proper citation: SNiPer-HD (RRID:SCR_004383) Copy
http://sourceforge.net/projects/vanator-cvr/
A Perl pipeline utilising a large variety of common alignment, assembly and analysis tools to assess the metagenomic profiles of Illumina deep sequencing samples. The emphasis is on the discovery of novel viruses in clinical and environmental samples.
Proper citation: Vanator (RRID:SCR_004370) Copy
http://www.csd.uwo.ca/~ilie/BOND/
Software program to compute highly specific DNA oligonucleotides, for all the genes that admit unique probes, while running orders of magnitude faster than the existing programs.
Proper citation: Basic OligoNucleotide Design (RRID:SCR_004492) Copy
https://wiki-bsse.ethz.ch/display/HSC/HelioScan+Home
HelioScan is a versatile control software for microscopes written in the intuitive graphical programming language LabVIEW. It solves a number of problems observed with custom-built image acquisition systems by providing the following features: * Extendability: both hardware components and software functionality are encapsulated in exchangeable, software components. Additional components can be implemented easily and plugged in at run-time. Components can be independently developed, allowing multiple developers to work in parallel. * Flexibility: Components are independently configurable; each component can have an unlimited number of configurations. * Understandability: The LabVIEW code is well-structured, commented and documented. * High speed: The software supports FPGA-based hardware that enables intelligent and extremely fast signal acquisition and generation. FPGA logic can be easily programmed using LabVIEW. * Tailored to in vivo brain imaging: The software is especially suited for 2-photon Calcium imaging, but can in principle be used for any kind of microscopy. The out-of-the-box software supports different imaging modalities (camera, galvanometric scan mirrors, acusto-optic deflectors) and imaging modes (camera video acquisition, intrinsic optical imaging, two-photon frame scan and tilted frame scan, 2D line scan, 3D spiral scan) and can easily be extended to other imaging modalities (e.g., resonance scanners), imaging modes (e.g., 2D and 3D arbitrary line scans) and associated hardware (e.g., stimulation devices). * Open file-format with extensible meta-data schema: HelioScan saves data in the OME-TIFF file format, which contains image data as multipage TIFF and meta-data as human-readable XML in the TIFF description tag according to the OME schema.
Proper citation: HelioScan (RRID:SCR_004494) Copy
http://www-pmr.ch.cam.ac.uk/wiki/Oscar3
OSCAR is software for the semantic annotation of chemistry papers. The modules OPSIN (a name to structure converter) and ChemTok (a tokeniser for chemical text) are also available as standalone libraries. This tool for shallow, chemistry-specific parsing of chemical documents identifies (or attempts to identify): * Chemical names: singular nouns, plurals, verbs etc., also formulae and acronyms, some enzymes and reaction names. * Ontology terms: if you can do it by string-matching, you can get OSCAR to do it. * Chemical data: Spectra, melting/boiling point, yield etc. in experimental sections. In addition, where possible the chemical names that are detected are annotated with structures, either via lookup or name-to-structure parsing (OPSIN), and with identifiers from the chemical ontology ChEBI Current work on OSCAR3 by Peter Corbett focuses on its use in SciBorg, a framework for the deep parsing of chemical text. OSCAR3 also includes the Oscar Server, a Jetty-powered set of servlets. These provide the following services: * Parsing of text/HTML by OSCAR. * Text/InChI/SMILES/SMILES substructues/SMILES similarity search of papers, coupled with keyword and ontology-based search, using Lucene and the CDK. * List of all names found / all names that co-occur with a search term or terms. * Online management of a chemical/stopword lexicon. * Manual editing of SciXML fragments containing named entities, for creating of gold standards and training data. Oscar3 can be found on SourceForge: http://sourceforge.net/projects/oscar3-chem/
Proper citation: Oscar3 (RRID:SCR_004561) Copy
http://metagenomics.atc.tcs.com/binning/SOrt-ITEMS/
Sequence orthology based software for improved taxonomic estimation of metagenomic sequences.
Proper citation: SOrt-ITEMS (RRID:SCR_004716) Copy
Located in the city of Galway in Ireland.
Proper citation: National University of Ireland; Galway; Ireland (RRID:SCR_004677) Copy
A multiple-sample, technology-aware SNP and indel caller.
Proper citation: UnifiedGenotyper (RRID:SCR_004710) Copy
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0075146
An R Package to Study Gene Spatial Neighbourhoods with Multi-Omics Annotations.
Proper citation: NuChart (RRID:SCR_004703) Copy
http://matsen.fhcrc.org/pplacer/
Software that places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis.
Proper citation: Pplacer (RRID:SCR_004737) Copy
Standalone software programs that can be used to calculate how well tetranucleotide usage patterns in DNA sequences correlate. Such correlations can provide valuable hints on the relatedness of DNA sequences.
Proper citation: TETRA (RRID:SCR_004573) Copy
Non-profit academic organization for research and services in bioinformatics. Provides freely available data from life science experiments, performs basic research in computational biology, and offers user training programme, manages databases of biological data including nucleic acid, protein sequences, and macromolecular structures. Part of EMBL.
Proper citation: European Bioinformatics Institute (RRID:SCR_004727) Copy
UKM affirms integration of faith in Allah and constructive knowledge along with amalgamation of theory and practice as core fundamentals in advancement of knowledge, building of educated society and development of university.
Proper citation: National University of Malaysia; Selangor; Malaysia (RRID:SCR_004724) Copy
http://www.researchgate.net/jobs/research/
Job board for science professionals worldwide. You may search through international listings in science and research or post your job listing for free. Advanced filters are available and you may also research jobs by field. Currently, fields include: Agricultural Science, Anthropology, Biology, Chemistry, Computer Science, Design, Economics, Education, Engineering, Entertainment and Arts, Geoscience, History, Law, Linguistics, Literature, Mathematics, Medicine, Other, Philosophy, Physics, Political Science, Psychology, Religious Studies, Social Science, Space Science
Proper citation: ResearchGate: Research Jobs (RRID:SCR_004641) Copy
https://sites.google.com/a/lbl.gov/biopig/
Software providing a framework for genomic data analysis using Apache Pig and Hadoop.
Proper citation: BioPig (RRID:SCR_004636) Copy
Drug discovery company providing pharma with protein and antibody therapeutics in the fields of Oncology and Immunology.
Proper citation: Compugen (RRID:SCR_004631) Copy
An independent, nonprofit organization focused on mammalian genetics research to advance human health. Their mission is to discover the genetic basis for preventing, treating, and curing human disease, and to enable research for the global biomedical community. Jackson Laboratory breeds and manages colonies of mice as resources for other research institutions and laboratories, along with providing software and techniques. Jackson Lab also conducts genetic research and provides educational material for various educational levels.
Proper citation: Jackson Laboratory (RRID:SCR_004633) Copy
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