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http://purl.bioontology.org/ontology/IDOBRU

A biomedical ontology in the domain of zoonotic disease brucellosis that is caused by Brucella, a facultative intracellular baterium.

Proper citation: Brucellosis Ontology (RRID:SCR_006795) Copy   

•   Source: SciCrunch Registry
  

http://www.ars-grin.gov/

Web server to provide germplasm information about plants, animals, microbes, invertebrates and access to databases that maintain passport, characterization, evaluation, inventory, and distribution data for the management and utilization of national germplasm collections. Under control of the U.S. Department of Agriculture's Agricultural Research Service to support the National Genetic Resources Program (NGRP). Operated by the Database Management Unit of the National Germplasm Resource Laboratory in Beltsville, Maryland.

Proper citation: Germplasm Resources Information Network (RRID:SCR_006675) Copy   

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https://itunes.apple.com/gb/app/neuropub-visualizer/id405721542?mt=8

A NIfTI visualizer for statistical brain images (fMRI, VBM, etc) the iPad. The visualizer displays these images as overlay on the MNI standard brain. You can use it to store all your statistical images from your fMRI / VBM / TBSS studies and visualise them in 2D and 3D. Use NeuroPub as a library for your statistical images. It's the perfect app to bring to meetings, conferences, etc, and show your latest results.

Proper citation: NeuroPub Visualizer (RRID:SCR_006797) Copy   

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http://redfly.ccr.buffalo.edu

Curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs). Includes experimentally verified fly regulatory elements along with their DNA sequence, associated genes, and expression patterns they direct. Submission of experimentally verified cis-regulatory elements that are not included in REDfly database are welcome.

Proper citation: REDfly Regulatory Element Database for Drosophilia (RRID:SCR_006790) Copy   

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https://github.com/friend1ws/EBCall

A software package for somatic mutation detection (including InDels). EBCall uses not only paired tumor/normal sequence data of a target sample, but also multiple non-paired normal reference samples for evaluating distribution of sequencing errors, which leads to an accurate mutaiton detection even in case of low sequencing depths and low allele frequencies.

Proper citation: EBCall (RRID:SCR_006791) Copy   

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http://cancer.cellmap.org

It is a collection of selected human-focused cellular pathways implicated in cancer that are linked to visualization and analysis tools. Biologists can browse and search the Cancer Cell Map pathways and view gene expression data on any pathway. All data is freely available. Computational biologists can download all pathways in BioPAX format for global analysis. Software developers can build software on top of the Cancer Cell Map using the web service API. Download and install the cPath pathway database software to create a local mirror of the Cancer Cell Map. Cancer Cell Map pathways were selected based on the scientific interests of research labs at Memorial Sloan-Kettering Cancer Center. Effort was made not to duplicate information in other public pathway databases. Available pathways include: Alpha6Beta4Integrin, AndrogenReceptor, EGFR1, Hedgehog, ID, KitReceptor, NOTCH, TGFBR, TNF alpha/NF-kB, Wnt. Each pathway has around 100-400 interactions.

Proper citation: Cancer Cell Map (RRID:SCR_006792) Copy   

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http://www.usrds.org/

Annual report, standard analysis files and an online query system from the national data registry on the end-stage renal disease (ESRD) population in the U.S., including treatments and outcomes. The Annual Data Report is divided into two parts. The Atlas section displays data using graphs and charts. Specific chapters address trends in ESRD patient populations, quality of ESRD care, kidney transplantation outcomes, costs of ESRD care, Healthy People 2010 objectives, chronic kidney disease, pediatric ESRD, and cardiovascular disease special studies. The Reference Tables are devoted entirely to the ESRD population. The RenDER (Renal Data Extraction and Referencing) online data query system allows users to build data tables and maps for the ESRD population. National, state, and county level data are available. USRDS staff collaborates with members of Centers for Medicare & Medicaid Services (CMS), the United Network for Organ Sharing (UNOS), and the ESRD networks, sharing datasets and actively working to improve the accuracy of ESRD patient information.

Proper citation: United States Renal Data System (RRID:SCR_006699) Copy   

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http://www.ebi.ac.uk/miriam/

A set of online services created in support of MIRIAM, a set of guidelines for the annotation and curation of computational models. The core of MIRIAM Resources is a catalogue of data types (namespaces corresponding to controlled vocabularies or databases), their URIs and the corresponding physical URLs or resources. Access to this data is made available via exports (XML) and Web Services (SOAP). MIRIAM Resources are developed and maintained under the BioModels.net initiative, and are free for use by all. MIRIAM Resources are composed of four components: a database, some Web Services, a Java library and this web application. * Database: The core of the system is a MySQL database. It allows us to store the data types (which can be controlled vocabularies or databases), their URIs and the corresponding physical URLs, and other details such as documentation and resource identifier patterns. Each entry contains a diverse set of details about the data type: official name and synonyms, root URI, pattern of identifiers, documentation, etc. Moreover, each data type can be associated with several resources (or physical locations). * Web Services: Programmatic access to the data is available via Web Services (based on Apache Axis and SOAP messages). In addition, REST-based services are currently being developed. This API allows one to not only resolve model annotations, but also to generate appropriate URIs, based upon the provision of a resource name and accession number. A list of available web services, and a WSDL are provided. A browser-based online demonstration of the Web Services is also available to try. * Java Library: A Java library is provided to access the Web Services. The documentation explains where to download it, its dependencies, and how to use it. * Web Application: A Web application, using an Apache Tomcat server, offers access to the whole data set via a Web browser. It is possible to browse by data type names as well as browse by tags. A search engine is also provided.

Proper citation: MIRIAM Resources (RRID:SCR_006697) Copy   

•   Source: SciCrunch Registry
  

https://www.nimhgenetics.org/

Collaborative venture between the National Institute of Mental Health (NIMH) and several academic institutions. Repository facilitates psychiatric genetic research by providing patient and control samples and phenotypic data for wide-range of mental disorders and Stem Cells.Stores biosamples, genetic, pedigree and clinical data collected in designated NIMH-funded human subject studies. RGR database likewise links to other repositories holding data from same subjects, including dbGAP, GEO and NDAR. Allows to access these data and biospecimens (e.g., lymphoblastoid cell lines, induced pluripotent cell lines, fibroblasts) and further expand genetic and molecular characterization of patient populations with severe mental illness.

Proper citation: NIMH Repository and Genomics Resources (RRID:SCR_006698) Copy   

•   Source: SciCrunch Registry
  

http://bactibase.pfba-lab-tun.org/main.php

Data repository of bacteriocin natural antimicrobial peptides and includes data collected from published literature as well as high-throughput datasets. The database provides a manually curated annotation of bacteriocin sequences. New bacteriocin submissions are welcome. Various tools have been incorporated for bacteriocin analysis, such as homology search, multiple sequence alignments, Hidden Markov Models, molecular modelling and retrieval through our taxonomy Browser. BACTIBASE should be a useful tool in food preservation or food safety applications and could have implications for the development of new drugs for medical use. BACTIBASE contains calculated or predicted physicochemical properties of 218 bacteriocins produced by both Gram-positive (194) and Gram-negative bacteria (19). They also note the presence of three bacteriocins from the Archaea domain. The database now comprises 31 genera (2009).

Proper citation: BACTIBASE (RRID:SCR_006694) Copy   

•   Source: SciCrunch Registry
  

http://inparanoid.sbc.su.se/cgi-bin/index.cgi

Collection of pairwise comparisons between 100 whole genomes generated by a fully automatic method for finding orthologs and in-paralogs between TWO species. Ortholog clusters in the InParanoid are seeded with a two-way best pairwise match, after which an algorithm for adding in-paralogs is applied. The method bypasses multiple alignments and phylogenetic trees, which can be slow and error-prone steps in classical ortholog detection. Still, it robustly detects complex orthologous relationships and assigns confidence values for in-paralogs. The original data sets can be downloaded.

Proper citation: InParanoid: Eukaryotic Ortholog Groups (RRID:SCR_006801) Copy   

•   Source: SciCrunch Registry
  

http://www.ebi.ac.uk/ontology-lookup/

Interactive and programmatic interfaces to query, browse and navigate an increasing number of biomedical ontologies and controlled vocabularies. It provides a web service interface to query multiple ontologies from a single location with a unified output format. It can integrate any ontology available in the Open Biomedical Ontology (OBO) format. The database can be queried to obtain information on a single term or to browse a complete ontology using AJAX. Auto-completion provides a user-friendly search mechanism. An AJAX-based ontology viewer is available to browse a complete ontology or subsets of it. A weekly MySQL database export file can be downloaded from the EBI public FTP directory.

Proper citation: Ontology Lookup Service (RRID:SCR_006596) Copy   

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http://sourceforge.net/projects/niftysim/

A high-performance nonlinear finite element solver. A key feature is the option of GPU-based execution, which allows the solver to significantly out-perform equivalent commercial packages.

Proper citation: NiftySim (RRID:SCR_006591) Copy   

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http://www.alexaplatform.org/alexa_seq/index.htm

A method for using massively parallel paired-end transcriptome sequencing for ''alternative expression analysis''.

Proper citation: ALEXA-Seq (RRID:SCR_006700) Copy   

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http://dally.nimh.nih.gov/matoff/matoff.html

An interactive analysis program that searches neurophysiological data and plots the results. MatOFF was developed especially for dealing with the complexities common to behavioral neurophysiological experiments. It runs under Windows 2000 or XP and relies on MATLAB version R11.1 (or above) for all operations. MatOFF searches a data file to locate and plot epochs (trials) of special interest to the investigator. Appropriate input data files have time-stamped event codes, usually including neuron action potential firing events (spikes), and digitized analog data. The user specifies a list of event code numbers that uniquely identify a sequence of events. MatOFF uses this sequence to search the raw data file, select the epochs that meet the criteria, time-shift the trials to align them on a common event, order the epochs based on user-selected criteria, and plot the results based on a collection of page formatting specifications. MatOFF will also save extracted data and some statistics to disk. Features: * Powerful, interactive searching tools for locating relevant experimental events * Compatible with Cortex data acquisition program * Compatible with Plexon data acquisition system * Flexible, publication-quality graphical display and printing * Comprehensive scripting language * Supports learning and other dynamic behavior * Integrated interface to MATLAB functions * Automatic alignment of trial data and generation of histograms * Large variety of options for selecting and ordering trial data * Descriptive and non-parametric statistics * XY analog displays * Data export with flexible format control * Up to 72 plots per page * Display templates can be saved and reloaded * Free for public or private use * Adaptable to almost any data file format

Proper citation: MatOFF (RRID:SCR_006821) Copy   

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http://sourceforge.net/projects/bmdexpress/

Bioinformatics tool used to analyze microarray dose-response data. The analysis provides benchmark dose estimates at which different cellular processes are altered in toxicogenomic experiments.

Proper citation: BMDExpress (RRID:SCR_006823) Copy   

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http://www.bioconductor.org/packages/2.11/bioc/html/ShortRead.html

Software package for input, quality assessment and exploration of high-throughput sequence data. Used for input, quality assurance, and basic manipulation of `short read'' DNA sequences such as those produced by Solexa, 454, and related technologies, including exible import of common short read data formats.

Proper citation: ShortRead (RRID:SCR_006813) Copy   

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http://compbio.bccrc.ca/software/mutationseq/

A software suite using feature-based classifiers for somatic mutation prediction from paired tumour/normal next-generation sequencing data. mutationSeq has the advantages of integrating different features (e.g., base qualities, mapping qualities, strand bias, and tailed distance features), and validated somatic mutations to make predictions. Given paired normal/tumour bam files, mutationSeq will output the probability of each candidate site being somatic.

Proper citation: mutationSeq (RRID:SCR_006815) Copy   

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http://www.uni-rostock.de/en/

Public university located in Rostock, Mecklenburg-Vorpommern, Germany. Founded in 1419.

Proper citation: University of Rostock; Mecklenburg-Vorpommern; Germany (RRID:SCR_006816) Copy   

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http://www.bioconductor.org/packages/2.12/bioc/html/RIPSeeker.html

A statistical software package for identifying protein-associated transcripts from RIP-seq experiments. Infer and discriminate RIP peaks from RIP-seq alignments using two-state HMM with negative binomial emission probability. While RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides a suite of bioinformatics tools integrated within this self-contained software package comprehensively addressing issues ranging from post-alignments processing to visualization and annotation.

Proper citation: RIPSeeker (RRID:SCR_006810) Copy   

•   Source: SciCrunch Registry