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http://www.hupo.org/

The Human Proteome Organisation (HUPO) is an international scientific organization representing and promoting proteomics through international cooperation and collaborations by fostering the development of new technologies, techniques and training.

Proper citation: HUPO - Human Proteome Organisation (RRID:SCR_010707) Copy   

•   Source: SciCrunch Registry
  

http://wanglab.pcbi.upenn.edu/coral/

A machine learning software package that can predict the precursor class of small RNAs present in a high-throughput RNA-sequencing dataset. In addition to classification, it also produces information about the features that are most important for discriminating different populations of small non-coding RNAs.

Proper citation: CoRAL - Classification of RNAs by Analysis of Length (RRID:SCR_010828) Copy   

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http://www.bcgsc.ca/platform/bioinfo/software/abyss

Software providing de novo, parallel, paired-end sequence assembler that is designed for short reads. ABySS 1.0 originally showed that assembling human genome using short 50 bp sequencing reads was possible by aggregating half terabyte of compute memory needed over several computers using standardized message passing system. ABySS 2.0 is Resource Efficient Assembly of Large Genomes using Bloom Filter. ABySS 2.0 departs from MPI and instead implements algorithms that employ Bloom filter, probabilistic data structure, to represent de Bruijn graph and reduce memory requirements.

Proper citation: ABySS (RRID:SCR_010709) Copy   

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http://compbio.cs.toronto.edu/CNVer/

A method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation.

Proper citation: CNVer (RRID:SCR_010820) Copy   

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http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0023501

An algorithm for de novo genome assembly with short paired-end reads.

Proper citation: Meraculous (RRID:SCR_010700) Copy   

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http://sv.gersteinlab.org/cnvnator/

An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.

Proper citation: CNVnator (RRID:SCR_010821) Copy   

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http://dictybase.org/teaching_tools/index.html

Dictyostelium discoideum is a great organism to use to teach cellular biology. It exhibits very interesting behaviors, such as chemotaxis and phagocytosis, that can readily be studied in standard laboratories without the need for expensive equipment. Lists of labs being used in real courses settings and all necessary information for performing those experiments are provided. Major headings: * Dictyostelium cell biology course, by Dr. David Knecht, University of Connecticut * Dictyostelium cell biology, by Dr. Derrick Brazill, Hunter College, New York * Report on the number of cells in a slug, contributed by John Bonner * Practical on chemotaxis, by Dr. Thierry Soldati, University of Geneva * Comments from Researchers * References suggested by contributors

Proper citation: dictyBase - Teaching Tools Using Dictyostelium discoideum (RRID:SCR_010701) Copy   

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http://bioinfo-out.curie.fr/projects/freec/tutorial.html

Prediction of copy number alterations and loss of heterozygosity using deep-sequencing data.

Proper citation: Control-FREEC (RRID:SCR_010822) Copy   

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http://code.google.com/p/readdepth/

This package for R can detect copy number aberrations by measuring the depth of coverage obtained by massively parallel sequencing of the genome.

Proper citation: readDepth (RRID:SCR_010824) Copy   

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http://www.nig.ac.jp/index-e.html

Institute for genetics, through National BioResource Project, collects, preserves, and provides bio-resources (strains, populations, tissues, cells, genes of animals, plants and microorganisms, and information on these materials for R&D use) that are essential for life science research.

Proper citation: National Institute of Genetics; Shizuoka; Japan (RRID:SCR_010836) Copy   

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http://bti.cornell.edu/

BTI is unique in being a private, not-for-profit research institute dedicated to plant biology, and located on a major university campus. Its mission is to advance and communicate scientific knowledge in plant biology to improve agriculture, protect the environment, and enhance human health. The institute was founded in Yonkers, New York, next to the home of its benefactor, William Boyce Thompson. In the mid-1970''s, however, it was recognized that a physical presence on a university campus would catapult the institute to a higher level of research, and the Cornell affiliation was born. BTI hires its own faculty, postdoctoral scholars and technicians, but also hosts undergraduate and graduate researchers from Cornell. BTI faculty generally have adjunct appointments at Cornell, and participate in graduate training and other university affairs. As envisioned in the Agreement of Affiliation, the partnership is advantageous for both parties, and contributes to a singularly strong environment for fundamental plant research on the campus. William Boyce Thompson founded BTI in 1924 on the premise that basic plant research leads to real benefits for people. Many potential applications of BTI research are to improve crops by increasing yield or nutritional content, or decreasing the need for harmful fertilizers and pesticides. Other research could lead to inexpensive plant-made vaccines, or even shed light on the human immune system. With aims like these in mind, scientists at BTI study life at the scale of genes and proteins to learn about processes such as how plants detect light, or how they respond when aphids bite into them. Along with research, BTI''s mission includes environmental responsibility and outreach to teachers, students, and community members. Though it remains an independent, non-profit institution, BTI is affiliated with Cornell University and is located on its Ithaca, New York campus.

Proper citation: Boyce Thompson Institute for Plant Research (RRID:SCR_010716) Copy   

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http://rth.dk/resources/rnasnp/

Software / Web Server to predict the effect of SNPs on local RNA secondary structure based on the RNA folding algorithms implemented in the Vienna RNA package.

Proper citation: RNAsnp (RRID:SCR_010837) Copy   

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http://compgenomics.utsa.edu/gene/gene_1.php

A Bayesian decision fusion algorithm for microRNA target prediction that combines the prediction of TargetScan, miRanda, PicTar, mirTarget, PITA, and DianamicroT. Users enter a Ref_seq ID for a query target gene and select a miRNA, which BCmicrO will use in its predictive algorithm. The prediction results can then be downloaded.

Proper citation: BCmicrO (RRID:SCR_010838) Copy   

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http://psidev.sourceforge.net/mi/xml/doc/user/index.html

The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics to facilitate data comparison, exchange and verification. As a first step, the PSI is developing standards for two key areas of proteomics: mass spectrometry and protein-protein interaction data. The document describes the molecular interaction data exchange format. PSI is following a leveled approach to building this specification. Level 1 will describe protein interactions at a basic level that covers a large amount of currently available data. Subsequent levels will add capability to represent new molecular interaction information that the community wishes to exchange. The scope of PSI MI is currently limited to protein-protein interactions. Other molecules, such as small molecules, DNA and RNA maybe taken into account in the future. The PSI MI format is a data exchange format for protein-protein interactions. It is not a proposed database structure. The purpose of the document is to describe the general structure of the PSI MI XML specification in a more user-friendly manner than the specification does itself. PSI MI was designed by a group of people including representatives from database providers and users in both academia and industry. PSI MI is supported by the DIP, MINT, IntAct, BIND and HPRD databases.

Proper citation: PSI-MI (RRID:SCR_010710) Copy   

•   Source: SciCrunch Registry
  

http://mirexpress.mbc.nctu.edu.tw/

A stand-alone software package implemented for generating miRNA expression profiles from high-throughput sequencing of RNA without the need for sequenced genomes.

Proper citation: miRExpress (RRID:SCR_010831) Copy   

•   Source: SciCrunch Registry
  

http://www.ntnu.edu/biotech/systembio

The new NTNU Systems Biology website showcases the different systems biology efforts at NTNU. Regular updates on new initiatives and advertisements for new PhD and Postdoc vacancies in systems biology will be posted.

Proper citation: NTNU Systems Biology (RRID:SCR_010713) Copy   

•   Source: SciCrunch Registry
  

http://www.mssm.edu/research/programs/manhattan-hiv-brain-bank/

Biorepository of tissues and fluids relevant for the neurologic, neuropsychologic, psychiatric and neuropathologic manifestations of HIV infection, linked to medical records and an on-going clinical trial for research use by the scientific community. The MHBB conducts a longitudinal, observational study that follows a group of HIV-infected individuals who have agreed to be fluid and organ donors for the purposes of AIDS research. They are currently the largest, multidisciplinary neuroAIDS cohort in New York City, the epicenter of the US HIV epidemic. Research participants undergo regular neurologic, neuropsychologic, and psychiatric evaluations, and provide body fluid samples that are linked to clinical information. Upon their demise, study participants become organ donors. This program has supplied clinical information, tissue, and fluid samples to over 70 qualified AIDS researchers across America, Europe and Australia. In fulfilling its resource mission, the MHBB functions as part of the National NeuroAIDS Tissue Consortium (NNTC). MHBB provides a means by which people living with HIV can be engaged in the struggle to improve our knowledge about HIV infection and the damage it causes to the body.

Proper citation: Manhattan HIV Brain Bank (RRID:SCR_010520) Copy   

•   Source: SciCrunch Registry
  

http://brainandsociety.org/the-brain-observatory

Formerly a topical portal studying the brain which collected and imaged 1000 human brains, the Brain Observatory has partnered with the Institute for Brain and Society to build virtual laboratories that will feed directly into the database of images and knowledge created in the context of the Human Brain Library. The Brain Observatory will also host exhibits, conferences, and events aimed at promoting a heightened awareness of brain research and how its results can benefit personal brain fitness and mental health.

Proper citation: Brain Observatory (RRID:SCR_010641) Copy   

•   Source: SciCrunch Registry
  

http://www.prabi.fr/

The PRABI is the Rhone-Alpes Bioinformatics Center, a IBISA platform member of the RENABI (the French network of bioinformatic platforms). It gathers 11 research teams spread on 4 different sites. The PRABI has research, service and training activities in a large number of bioinformatics and biostatistics fields.

Proper citation: PRABI (RRID:SCR_010522) Copy   

•   Source: SciCrunch Registry
  

http://compbio.cs.toronto.edu/modil/

Software for a novel method for finding medium sized indels from high throughput sequencing datasets.

Proper citation: MoDIL (RRID:SCR_010764) Copy   

•   Source: SciCrunch Registry