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Software for short-read mapping to accurately map reads from the next-generation sequencing technology. It can map reads with or without error probability information (quality scores) and supports paired-end reads or bisulfite-treated reads mapping. There is no limitaions on read widths or number of mismatches. RMAP can now map more than 8 million reads in an hour at full sensitivity to 2 mismatches.
Proper citation: RMAP (RRID:SCR_000695) Copy
https://github.com/iontorrent/TMAP
Alignment software for short and long nucleotide sequences produced by next-generation sequencing technologies.
Proper citation: TMAP (RRID:SCR_000687) Copy
http://franklin.imgen.bcm.tmc.edu/
The mission of the Baylor College of Medicine - Shaw Laboratory is to apply methods of statistics and bioinformatics to the analysis of large scale genomic data. Our vision is data integration to reveal the underlying connections between genes and processes in order to cure disease and improve healthcare.
Proper citation: Baylor College of Medicine - Shaw Laboratory (RRID:SCR_000604) Copy
Laboratory portal of the University of Sao Paulo Molecular Genetics and Bioinformatic Laboratory.
Proper citation: USP Molecular Genetics and Bioinformatics Laboratory (RRID:SCR_000605) Copy
A commercial vendor of chemicals that provides custom synthesis of a wide variety of organic compounds. Frontier Scientific has capabilities for custom work in organoborons, organotins, porphyrins, silanes, halogenations, catalysts and cross couplings using Suzuki, Stille, and Kumada processes.
Proper citation: Frontier Scientific Chemical Supplier (RRID:SCR_000914) Copy
University in Scotland, UK that provides undergraduate and doctoral degree programs.
Proper citation: University of Dundee; Scotland; United Kingdom (RRID:SCR_000997) Copy
Private research university in Medford and Somerville, Massachusetts, United States, with additional facilities in Boston and Grafton, as well as Talloires, France. Provides undergraduate, graduate, and professional degree programs.
Proper citation: Tufts University; Massachusetts; USA (RRID:SCR_000994) Copy
Pasteur Institute of Lille is an international research institute in Lille, France focused on bettering human health by detecting risk factors in degenerative diseases.
Proper citation: Pasteur Institute of Lille; Lille; France (RRID:SCR_000990) Copy
http://www.ced.co.uk/pru.shtml?spk7wglu.htm
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 23,2022. A data acquisition and analysis software package for electrophysiology data. Spike2 software offers multi-channel continuous data acquisition and analysis with a multitude of options. This offers flexible usage from a simple chart recorder to complex applications requiring stimulus generation, data capture, scrolling or triggered displays, control of external equipment, and custom analysis. Spike2 software can be used in many fields such as electrophysiology, neurophysiology, cardiovascular and respiratory studies, sports science and pharmacology.
Proper citation: Spike2 Software (RRID:SCR_000903) Copy
The Office of Research on Women's Health (ORWH) is part of the Office of the Director of NIH. ORWH works in partnership with the 27 NIH Institutes and Centers to ensure that women’s health research is part of the scientific framework at the NIH and throughout the scientific community.
Proper citation: NIH Office of Research on Women's Health; Bethesda; Maryland (RRID:SCR_000986) Copy
A configurable, open-source, Nipype-based, automated processing pipeline for resting state functional MRI (R-fMRI) data, for use by both novice and expert users. C-PAC was designed to bring the power, flexibility and elegance of the Nipype platform to users in a plug and play fashion?without requiring the ability to program. Using an easy to read, text-editable configuration file, C-PAC can rapidly orchestrate automated R-fMRI processing procedures, including: - quality assurance measurements - image preprocessing based upon user specified preferences - generation of functional connectivity maps (e.g., correlation analyses) - customizable extraction of time-series data - generation of local R-fMRI metrics (e.g., regional homogeneity, voxel-matched homotopic connectivity, fALFF/ALFF) C-PAC makes it possible to use a single configuration file to launch a factorial number of pipelines differing with respect to specific processing steps.
Proper citation: C-PAC (RRID:SCR_000862) Copy
http://www.ntu.edu.tw/english/
A national research university in Taipei, Taiwan. The university confers degrees at the undergraduate and graduate level bio-resources and agriculture, electrical engineering and computer science, engineering, law, liberal arts, management, medicine, public health, and the social sciences.
Proper citation: National Taiwan University; Taipei; Taiwan (RRID:SCR_000983) Copy
A public university located in Singapore that has a wide range of faculties and schools, including arts, business, computing, and dentistry.
Proper citation: National University of Singapore; Singapore; Singapore (RRID:SCR_000984) Copy
http://code.google.com/hosting/
Project Hosting on Google Code provides a free collaborative development environment for open source projects.
Proper citation: Google Project Hosting (RRID:SCR_000811) Copy
A non-profit organization that supports the advance of healthy aging through biomedical research.
Proper citation: American Federation for Aging Research (RRID:SCR_000806) Copy
https://www.openbiosystems.com/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. Open Biosystems offers products that span Genomics, RNAi and Antibodies. Building on the rapid sharing model that is at the core of the Human Genome Project, Open Biosystems collaborates with some of the most innovative life science investigators working today. We partner with them to bring to market new productsthey have often pioneered the new resources in their own lab, and we prepare it for widespread use and then provide access to the research community. Delivery of genetic content is our most recent technological breakthrough. Recently, we brought to market the Tranz-vector system, the safest human-based lentiviral delivery technology. Further supplementing our already strong line of RNA interference (RNAi) and complementary DNA (cDNA) products, this technology provides investigators with superior delivery capabilities for high-quality cellular screening. The combination or our unique Tranz-vector system and whole genome RNAi and cDNA content enables our customers to perform drug target validation on a large scale. With our genomics resources, Open Biosystems provides the content investigators utilize to unlock the functions of human genes and their relationships to normal and disease development. We offer the most complete gene library in the industry. This novel library consists of several full length cDNA and open reading frame collections. Most prominently among these is the Mammalian Gene Collection (MGC), the industry's gold standard gene catalog. The discovery of RNA interference has revolutionized the way investigators approach the studies of gene expression, regulation and interactions, particularly as it relates to drug development. Our collaboration with Drs. Greg Hannon (CSHL) and Steve Elledge (Harvard) has led the way in the evolution of the short hairpin RNA (shRNA) technologies to provide the life science community with whole genome resources for human, mouse and rat with a multitude of technology and delivery advantages.
Proper citation: Open Biosystems (RRID:SCR_000808) Copy
An Italian private research university that offers undergraduate, graduate and postdoctoral level degrees in both Italian and English.
Proper citation: Catholic University of the Sacred Heart; Milan; Italy (RRID:SCR_000958) Copy
An Australian government agency that allocates research funding to academics and researchers at Australian universities. The mission of the council is to deliver policy and programs that advance Australian research, spur innovation and benefit the community.
Proper citation: Australian Research Council (RRID:SCR_000952) Copy
A lab organization which has bases in Munich, Germany and at Columbia University and focuses its research on protein structure and function using sequence and evolutionary information. They utilize machine learning and statistical methods to analyze genetic material and its gene products. Research goals of the lab involve using protein and DNA sequences along with evolutionary information to predict aspects of the proteins relevant to the advance of biomedical research.
Proper citation: ROSTLAB (RRID:SCR_000792) Copy
International collaborative research project and database of annotated mammalian genome. Used to improve estimates of total number of genes and their alternative transcript isoforms in both human and mouse. Consortium to assign functional annotations to full length cDNAs that were collected during Mouse Encyclopedia Project at RIKEN.
Proper citation: Functional Annotation of the Mammalian Genome (RRID:SCR_000788) Copy
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