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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
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
Commercial supplier and developer of in vivo antibodies. Provides antibodies and antibody production services.
Proper citation: Bio X Cell (RRID:SCR_004997) Copy
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
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
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
http://noble.gs.washington.edu/proj/percolator/
Percolator post-processes the results of a shotgun proteomics database search program, re-ranking peptide-spectrum matches so that the top of the list is enriched for correct matches. Shotgun proteomics uses liquid chromatography-tandem mass spectrometry to identify proteins in complex biological samples. We describe an algorithm, called Percolator, for improving the rate of peptide identifications from a collection of tandem mass spectra. Percolator uses semi-supervised machine learning to discriminate between correct and decoy spectrum identifications, correctly assigning peptides to 17% more spectra from a tryptic dataset and up to 77% more spectra from non-tryptic digests, relative to a fully supervised approach. The yeast-01 data is available in tab delimetered format. The SEQUEST parameter file and target database for the yeast and worm data are also available.
Proper citation: Percolator: Semi-supervised learning for peptide identification from shotgun proteomics datasets (RRID:SCR_005040) Copy
Portal touching on all aspects of neuroscience from molecules to the mind, from the laboratory bench to the patient's bedside. Members study the normal structure and workings of the nervous system, its development, its cognitive functions, its derangement by disease and injury, and the means of its repair and protection. Projects span traditional disciplinary boundaries, as do graduate and postdoctoral training programs. Its major achievement has been to foster and improve multidisciplinary collaborations which has increasingly permitted the identification of pathogenic mechanisms and the formulation of new therapeutic approaches.
Proper citation: Brain Research Institute (RRID:SCR_004988) Copy
http://health.usf.edu/byrd/adrc/index.htm
A statewide consortium dedicated to Alzheimer's disease research to better understand the disease and related memory disorders. It includes Alzheimer's researchers and clinicians from institutions across Florida such as USF Health, Mayo Clinic Jacksonville, and Mount Sinai Medical Center. The purpose of the ADRC is to assist institutions in developing an infrastructure (cores) that can be used for various research projects with the goal of better understanding Alzheimer's disease and related disorders. The Florida ADRC is comprised of six cores, three projects and three pilot projects among other collaborations that utilize these cores.
Proper citation: Florida Alzheimer's Disease Research Center (RRID:SCR_004940) Copy
http://cran.r-project.org/web/packages/MBCluster.Seq/index.html
Software to cluster genes based on Poisson or Negative-Binomial model for RNA-Seq or other digital gene expression (DGE) data.
Proper citation: MBCluster.Seq (RRID:SCR_005079) Copy
Public research university with its main campus in Lawrence, Kansas, and several satellite campuses, research and educational centers, medical centers, and classes across the state of Kansas.
Proper citation: University of Kansas; Kansas; USA (RRID:SCR_005075) Copy
http://www.biomedcentral.com/1471-2105/13/189
An algorithm to use optical map information directly within the de Bruijn graph framework to help produce an accurate assembly of a genome that is consistent with the optical map information provided. AGORA takes as input two data structures: OpMap ? an ordered list of fragment sizes representing the optical map; and Edges ? a list of de Bruijn graph edges with their corresponding sequences.
Proper citation: AGORA (RRID:SCR_005070) Copy
https://github.com/AlexeyG/GRASS
A generic algorithm for scaffolding next-generation sequencing assemblies.
Proper citation: GRASS (RRID:SCR_005071) Copy
http://www.protocol-online.org/
Database of research protocols in a variety of life science fields, it contains protocols contributed by worldwide researchers as well as links to web protocols hosted by worldwide research labs, biotech companies, personal web sites. The data is stored in a MySql relational database. Protocol Online also hosts discipline specific discussion forums (BioForum), and provides a free PubMed search and alerting service (PubAlert).
Proper citation: Protocol Online - Your labs reference book (RRID:SCR_004937) Copy
http://www.bioinf.boku.ac.at/pub/MapAl/
A software tool for RNA-Seq expression profiling that builds on the established programs Bowtie and Cufflinks. Allowing an incorporation of ''gene models'' already at the alignment stage almost doubles the number of transcripts that can be measured reliably.
Proper citation: MapAl (RRID:SCR_004938) Copy
Public research university and the largest university in the UK for undergraduate education. The majority of the OU's undergraduate students are based in the United Kingdom and principally study off-campus; many of its courses can also be studied anywhere in the world.
Proper citation: Open University; Milton Keynes; United Kingdom (RRID:SCR_004931) Copy
http://www.arb-silva.de/aligner/
Service to align and optionally taxonomically classify your rRNA gene sequences. The results can be combined with any other sequences aligned by SINA or taken from the SILVA databases by concatenation of FASTA files or using the ARB MERGE tool. Note: Submission is currently limited to at most 1000 sequences of at most 6000 bases each. If your requirements exceed this limitation, get Opens internal link in current windowSINA for local installation.
Proper citation: SINA (RRID:SCR_005067) Copy
http://sourceforge.net/apps/mediawiki/amos/index.php?title=Bambus2
Software for scaffolding to address some of the challenges encountered when analyzing metagenomes. Scaffolding represents the task of ordering and orienting contigs by incorporating additional information about their relative placement along the genome. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny.
Proper citation: Bambus (RRID:SCR_005068) Copy
Neuron Navigator (NNG) integrates a 3D neuron image database into an easy-to-use visual interface. Via a flexible and user-friendly interface, NNG is designed to help researchers analyze and observe the connectivity within the neural maze and discover possible pathways. With NNG''s 3D neuron image database, researchers can perform volumetric searches using the location of neural terminals, or the occupation of neuron volumes within the 3D brain space. Also, the presence of the neurons under a combination of spatial restrictions can be shown as well. NNG is a result of a multi-discipline collaboration between neuroscientists and computer scientists, and NNG has now been implemented on a coordinated brain space for the Drosophila (fruit fly) brain. Account is required.
Proper citation: Neuron Navigator (RRID:SCR_005063) Copy
http://www.medicine.uiowa.edu/
Medical school of the University of Iowa, located in Iowa City, in the U.S. state of Iowa.
Proper citation: University of Iowa Carver College of Medicine; Iowa; USA (RRID:SCR_005064) Copy
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