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http://bowtie-bio.sourceforge.net/index.shtml

Software ultrafast memory efficient tool for aligning sequencing reads. Bowtie is short read aligner.

Proper citation: Bowtie (RRID:SCR_005476) Copy   

•   Source: SciCrunch Registry

http://carringtonlab.org/resources/cashx

Software pipeline to parse, map, quantify and manage large quantities of sequence data. CASHX is a set of tools that can be used together, or as independent modules on their own. The reference genome alignment tools can be used with any reference sequence in fasta format. The pipeline was designed and tested using Arabidopsis thaliana small RNA reads generated using an Illumina 1G.

Proper citation: CASHX (RRID:SCR_005477) Copy   

•   Source: SciCrunch Registry

http://www.labman.org

On March 8, 2008 in Havana, the Latin American Network for Brain Mapping (LABMAN) was created with participants from Argentina, Brazil, Colombia, Cuba and Mexico. The focus of LABMAN is to promote neuroimaging and systems neuroscience in the region through the implementation of training and exchange programs, and to increase public awareness of the Latin American potential to contribute both to basic and applied research in human brain mapping. The immediate LABMAN goals are to: * Train specialists in all major imaging techniques. * Expedite the transfer of new scientific and technical knowledge from abroad. * Increase the scientific productivity of the region. * Drastically increase the awareness of local governments, international organizations and of the general public of brain mapping results on potential. * Organize multinational projects in areas of special relevance to the region, e.g. nutrition, pediatric development, neurodegeneration. Latin American Brain Mapping Network (LABMAN) participants : * Cuban Neuroscience Center * University of Buenos Aires * University of Sao Paulo * Universidad del Valle, Cal��, Colombia * UAM Iztapalapa, Mexico City, Mexico

Proper citation: Latin American Brain Mapping Network (LABMAN) (RRID:SCR_005509) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/p/treq/home/Home/

A software read mapper for high-throughput DNA sequencing reads, in particular one to several hundred nucleotides in length, and for large edit distance between sequencing read and match in the reference genome. It can cope particularly well with indels for single-best hit recall of 200nt reads simulated from the human reference genome. TreQ performs best at a running time comparable to BWA at large edit distance settings.

Proper citation: TreQ (RRID:SCR_005505) Copy   

•   Source: SciCrunch Registry

http://microbesonline.org/

MicrobesOnline is designed specifically to facilitate comparative studies on prokaryotic genomes. It is an entry point for operon, regulons, cis-regulatory and network predictions based on comparative analysis of genomes. The portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms ranging from model organisms such as Escherichia coli and Saccharomyces cerevisiae to environmental microbes such as Desulfovibrio vulgaris and Shewanella oneidensis. To assist in annotating genes and in reconstructing their evolutionary history, MicrobesOnline includes a comparative genome browser based on phylogenetic trees for every gene family as well as a species tree. To identify co-regulated genes, MicrobesOnline can search for genes based on their expression profile, and provides tools for identifying regulatory motifs and seeing if they are conserved. MicrobesOnline also includes fast phylogenetic profile searches, comparative views of metabolic pathways, operon predictions, a workbench for sequence analysis and integration with RegTransBase and other microbial genome resources. The next update of MicrobesOnline will contain significant new functionality, including comparative analysis of metagenomic sequence data. Programmatic access to the database, along with source code and documentation, is available at http://microbesonline.org/programmers.html.

Proper citation: MicrobesOnline (RRID:SCR_005507) Copy   

•   Source: SciCrunch Registry

http://www.udl.cat/ca/

University based in Lleida, Spain. It was the first university in Catalonia and the whole Crown of Aragon. It was founded in 1300, using the name of Estudi General de Lleida.Leading institution in Spain for research and education in the fields of Agronomy, Food Technology and Forestry.

Proper citation: University of Lleida; Lleida; Spain (RRID:SCR_005500) Copy   

•   Source: SciCrunch Registry

http://www.idi.mineco.gob.es/portal/site/MICINN/

Proper citation: Spanish Ministry of Science and Innovation (RRID:SCR_011533) Copy   

•   Source: SciCrunch Registry

http://www.stjames.ie/

Teaching hospital in Dublin, Ireland. Its academic partner is Trinity College Dublin. It is managed by Dublin Midlands Hospital Group.

Proper citation: St. James Hospital; Dublin; Ireland (RRID:SCR_011535) Copy   

•   Source: SciCrunch Registry

http://www.sp.se/en/units/sppd/

A national research institute focusing on chemical, biochemical and pharmaceutical process development. Their main task is to build, use and provide expertise to increase success rates for academic and industrial actors with the development of new products and production processes. The institute forms an important resource and competence platform for knowledge generation, knowledge transfer, concept testing and risk sharing. Via SP Process Development, researchers and small and medium- sized enterprises (SMEs ) are provided access to tools, technology, equipment and complementing specialist knowledge. Sections that constitute the institute: * Analysis and Solid State * Catalysis * Process Development and Crystallization * Substance and Formulation What they do * Bringing together academia and industry to solve challenges within chemical, biochemical, technical and medical applications * Helping SMEs and academic research groups to drive ideas from the laboratory to commercial application * Enabling companies from different industries to increase collaboration regarding mutual challenges * Communicating challenges and requirements from industry to academic research groups

Proper citation: SP Process Development; Sodermanland; Sweden (RRID:SCR_011536) Copy   

•   Source: SciCrunch Registry

http://english.hi.is/

Public research university in Reykjavík, Iceland and the country's oldest and largest institution of higher education.

Proper citation: University of Iceland; Reykjavik; Iceland (RRID:SCR_011657) Copy   

•   Source: SciCrunch Registry

http://med.stanford.edu/

Medical school of Stanford University and is located in Stanford, California. It traces its roots to the Medical Department of the University of the Pacific, founded in San Francisco in 1858.

Proper citation: Stanford University School of Medicine; California; USA (RRID:SCR_011539) Copy   

•   Source: SciCrunch Registry

http://www.uic.edu/

Public research university in Chicago, Illinois. Its campus is in the Near West Side community area, adjacent to the Chicago Loop.

Proper citation: University of Illinois at Chicago; Illinois; USA (RRID:SCR_011660) Copy   

•   Source: SciCrunch Registry

http://www.sun.ac.za/english

Public research university situated in Stellenbosch, a town in the Western Cape province of South Africa.

Proper citation: Stellenbosch University; Western Cape; South Africa (RRID:SCR_011541) Copy   

•   Source: SciCrunch Registry

http://www.umd.edu/

Public research university in College Park, Maryland. Founded in 1856, UMD is the flagship institution of the University System of Maryland.

Proper citation: University of Maryland; Maryland; USA (RRID:SCR_011662) Copy   

•   Source: SciCrunch Registry

http://www.sll.se/sll/templates/NormalPage.aspx?id=19

The County Council is responsible for all publicly-financed healthcare and public transport in Stockholm County. The County Council is also responsible for other overall issues within the county, such as regional planning and cultural subsidies. Sweden''s political system has three democratically elected levels. At national level there is Parliament and the Government, at regional level there are county councils/regions, and at local level there are municipalities. The state decides on the laws and regulations that govern the work of county councils/regions and municipalities. healthcare, public transport and regional development the County Council''s broad responsibility

Proper citation: Stockholm County Council (RRID:SCR_011542) Copy   

•   Source: SciCrunch Registry

http://www.stonybrook.edu/

Public sea grant and space grant research university in Stony Brook, New York. It is one of four university centers of the State University of New York system.

Proper citation: Stony Brook University; New York; USA (RRID:SCR_011545) Copy   

•   Source: SciCrunch Registry

http://www.miami.edu/

Private research university in Coral Gables, Florida.

Proper citation: University of Miami; Florida; USA (RRID:SCR_011666) Copy   

•   Source: SciCrunch Registry

http://www.sgul.ac.uk/

A specialist medical and health sciences college and part of the University of London.

Proper citation: St Georges University of London; London; United Kingdom (RRID:SCR_011547) Copy   

•   Source: SciCrunch Registry

http://www.upstate.edu/

Public medical school in Syracuse, New York. It is part of the State University of New York system.

Proper citation: SUNY Upstate Medical University; New York; USA (RRID:SCR_011549) Copy   

•   Source: SciCrunch Registry

http://www.vr.se/inenglish.4.12fff4451215cbd83e4800015152.html

Government agency in Sweden established in 2001, with the responsibility to support and develop basic scientific research. Its objective is for Sweden to be a leading nation in scientific research.

Proper citation: Swedish Research Council (RRID:SCR_011552) Copy   

•   Source: SciCrunch Registry