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http://www.imgt.org/IMGTrepertoire/

Web resource for immunoglobulins (IG), T cell receptors (TR) and major histocompatibility (MH) and related proteins of immune system (RPI). Comprises LIGM expertized data on immunoglobulins (IG), T cell receptors (TR) and major histocompatibility (MH) and related proteins of immune system.

Proper citation: IMGT Repertoire (RRID:SCR_018220) Copy   

•   Source: SciCrunch Registry

https://t1dexchange.org/pages/

Provides access to resources T1D researchers need to conduct clinical studies. Data sets from their clinic registry is openly available, as are new study results. They also offer use of T1D Discovery Tool, which allows users to search different fields from registry data, and T1D Exchange Biobank, which offers specimen types such as serum, plasma, white blood cells, DNA, and RNA.

Proper citation: T1D Exchange (RRID:SCR_014532) Copy   

•   Source: SciCrunch Registry

https://www.jax.org/research-and-faculty/resources/knockout-mouse-project

Information from JAX about their contributions to KOMP project coordinated by International Mouse Phenotyping Consortium. National Institutes of Health has funded three KOMP2 centers in United States, including one at Jackson Laboratory, to work together on task of producing and phenotyping mice to establish resource of knockout mice and related database of gene function.

Proper citation: Knockout Mouse Project Repository at JAX (RRID:SCR_017512) Copy   

•   Source: SciCrunch Registry

http://medblast.sibsnet.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. An algorithm that finds articles most relevant to a genetic sequence. In the genomic era, researchers often want to know more information about a biological sequence by retrieving its related articles. However, there is no available tool yet to achieve conveniently this goal. Here, a new literature-mining tool MedBlast is developed, which uses natural language processing techniques, to retrieve the related articles of a given sequence. An online server of this program is also provided. The genome sequencing projects generate such a large amount of data every day that many molecular biologists often encounter some sequences that they know nothing about. Literature is usually the principal resource of such information. It is relatively easy to mine the articles cited by the sequence annotation; however, it is a difficult task to retrieve those relevant articles without direct citation relationship. The related articles are those described in the given sequence (gene/protein), or its redundant sequences, or the close homologs in various species. They can be divided into two classes: direct references, which include those either cited by the sequence annotation or citing the sequence in its text; indirect references, those which contain gene symbols of the given sequence. A few additional issues make the task even more complicated: (1) symbols may have aliases; and (2) one sequence may have a couple of relatives that we want to take into account too, which include redundant (e.g. protein and gene sequences) and close homologs. Here the issues are addressed by the development of the software MedBlast, which can retrieve the related articles of the given sequence automatically. MedBlast uses BLAST to extend homology relationships, precompiled species-specific thesauruses, a useful semantics technique in natural language processing (NLP), to extend alias relationship, and EUtilities toolset to search and retrieve corresponding articles of each sequence from PubMed. MedBlast take a sequence in FASTA format as input. The program first uses BLAST to search the GenBank nucleic acid and protein non-redundant (nr) databases, to extend to those homologous and corresponding nucleic acid and protein sequences. Users can input the BLAST results directly, but it is recommended to input the result of both protein and nucleic acid nr databases. The hits with low e-values are chosen as the relatives because the low similarity hits often do not contain specific information. Very long sequences, e.g. 100k, which are usually genomic sequences, are discarded too, for they do not contain specific direct references. User can adjust these parameters to meet their own needs.

Proper citation: MedBlast (RRID:SCR_008202) Copy   

•   Source: SciCrunch Registry

http://www.archer.edu.au/

The ARCHER project is built upon the prototype software developed by the DART (http://dart.edu.au) and ARROW (http://arrow.edu.au) projects to produce a robust set of software tools. These tools: - may be customised to suit the needs of diverse research areas - automate the collection and management of instrument generated data - enable the repository storage of research data and associated metadata - enable collection and tagging of research data in a collaborative environment, and - provide these capabilities in a secure end-to-end proces. :ARCHER developed a ''production-ready'' software tools, operating in a secure environment, to assist researchers to: - collect, capture and retain large data sets from a range of different sources including scientific instruments - deposit data files and data sets to eResearch storage repositories - populate these eResearch data repositories with associated metadata - permit data set annotation and discussion in a collaborative environment, and - support next-generation methods for research publication, dissemination and access.

Proper citation: Australian ResearCH Enabling enviRonment (RRID:SCR_008390) Copy   

•   Source: SciCrunch Registry

http://www.affymetrix.com/support/developer/powertools/apt_archive.affx

Affymetrix Power Tools (APT) are a set of cross-platform command line programs that implement algorithms for analyzing and working with Affymetrix GeneChip arrays. APT programs are intended for power users who prefer programs that can be utilized in scripting environments and are sophisticated enough to handle the complexity of extra features and functionality. APT provides platform for developing and deploying new algorithms without waiting for the GUI implementations. This resource is supported by Affymetrix, Inc.

Proper citation: Affymetrix Power Tools (RRID:SCR_008401) Copy   

•   Source: SciCrunch Registry

http://tuna.tamu.edu

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. Map improvement server that returns a bias minimized, 6-fold averaged map generated from a model and diffraction data (with optional preceding Molecular Replacement). It does not build or repair the model for you (yet). For automated model building, you need to install a local copy of CCP4 and ARP/wARP (aka wARP&Trace), RESOLVE, MAID, or TEXTAL.

Proper citation: TB Consortium Bias Removal Server (RRID:SCR_008425) Copy   

•   Source: SciCrunch Registry

http://openii.sourceforge.net/

OpenII (pronounced open-eye-eye) is a freely downloadable, open source information integration (II) tool suite. It includes 1) an extensible, plug-and-play platform for II tools and 2) several tools that assist with common integration tasks, including fully- or semi-automated support in the following scenarios: :- An integration engineer building a data warehouse must determine how diverse component data schemas map to the schema of the warehouse. :- An XML document that conforms to one schema needs to be converted into an equivalent document that conforms to a second (different) schema. :- To support data exchanges, a community needs to create a shared data model based on the models of its members. When a new member joins, the community needs to identify promising data exchange partners, and to what extent its shared model needs to be extended. Similarly, a chief information officer must identify data integration opportunities and make level-of-effort estimates after an acquisition or merger. To support these scenarios, OpenII provides a schema repository into which diverse data models can easily be imported. It also provides tools that 1) assist with identifying semantic correspondences across data models (Harmony), 2) compare a set of data models against a common reference model (Proximity), 3) visually organize a set of data models into clusters of related data models (Affinity), and 4) establish a common data model for a set of inter-related data models (Unity). Why should You use OpenII? Here are some reasons: :- OpenII is the only open-source platform for information integration tools. OpenII and its source code are freely available using the Apache 2.0 license, so you are free to borrow, extend or resell any portions of OpenII. :- The OpenII schema and mapping repository is based on a neutral modeling language. Thus, all of the OpenII tools can be used regardless of the underlying modeling language. For example, Harmony can identify correspondences among an XML schema, a relational database, and an OWL ontology. By comparison, most commercial tools are tied to a particular modeling language. :- OpenII is based on the Eclipse framework. As a result, the environment is already familiar to many programmers. Non-programmers can choose, instead, to use OpenII off-the-shelf without needing to first install Eclipse. :- OpenII is fully extensible. If needed components do not exist, they can be readily added. For example, adding a new importer or exporter is a straightforward task that can be completed in only a few hours. Moreover, each of the tools supports the introduction of new algorithms. And, programmers familiar with the Eclipse environment can add new views with moderate effort. Sponsors: This resource is supported by the MITRE Corporation.

Proper citation: Open Information Integration (RRID:SCR_008699) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/

Non profit research organization for genome sequences to advance understanding of biology of humans and pathogens in order to improve human health globally. Provides data which can be translated for diagnostics, treatments or therapies including over 100 finished genomes, which can be downloaded. Data are publicly available on limited basis, and provided more extensively upon request.

Proper citation: Wellcome Trust Sanger Institute; Hinxton; United Kingdom (RRID:SCR_011784) Copy   

•   Source: SciCrunch Registry

http://www.ime.fraunhofer.de/en.html

Provides assistance with consulting on experimental design, training on bioinformatics tools and databases, data quality assessment, data processing, data visualization, data interpretation, data mining of published datasets, and assistance with preparation of manuscripts and grant proposals.

Proper citation: Mainz Institute of Molecular Biology Bioinformatics Core Facility (RRID:SCR_011244) Copy   

•   Source: SciCrunch Registry

https://alleninstitute.org/

Non profit bioscience research organization in Seattle, Washington dedicated to accelerating research globally and sharing that data within the science community. Allen Institute for Brain Science, Allen Institute for Cell Science, Allen Institute for Immunology, and The Paul G. Allen Frontiers Group are four divisions of this Institute with commitment to open science model within its research institutes.

Proper citation: Allen Institute (RRID:SCR_005435) Copy   

•   Source: SciCrunch Registry

http://eddylab.org/software.html

Software library containing tools for statistical manipulations of data. Tools include profile hidden Markov models for biological sequence analysis, RNA structure analysis, and a prototype noncoding RNA genefinder.

Proper citation: Eddy Lab Software (RRID:SCR_001458) Copy   

•   Source: SciCrunch Registry

http://www.incf.org/

Independent international facilitator catalyzing and coordinating global development of neuroinformatics aiming to advance data reuse and reproducibility in global brain research. Integrates and analyzes diverse data across scales, techniques, and species to understand brain function and positively impact the health and well being of society.

Proper citation: International Neuroinformatics Coordinating Facility (RRID:SCR_002282) Copy   

•   Source: SciCrunch Registry

https://dans.knaw.nl/en

Netherlands institute for permanent access to digital research resources. DANS encourages researchers to make their digital research data findable, accessible, interoperable and reusable. It does this by providing expert advice and certified services.

Proper citation: DANS (RRID:SCR_000904) Copy   

•   Source: SciCrunch Registry

http://www.mayo.edu/research/departments-divisions/department-health-sciences-research/division-biomedical-statistics-informatics/software/bioinformatics-software-packages

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18,2023. A free bioinformatics software tool to help identify fusion transcripts from paired-end transcriptome sequencing data. The source codes of SnowShoes-FTD are provided in two formats: one configured to run on the Sun Grid Engine for parallelization with shorter run time, and the other formatted to run on a single LINUX node.

Proper citation: SnowsShoes-FTD (RRID:SCR_000076) Copy   

•   Source: SciCrunch Registry

http://soap.genomics.org.cn/SOAPfusion.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 22,2022. An open source software tool for fusion discovery with paired-end RNA-Seq reads. The tool follows a different strategy by finding fusions directly and verifying them, differentiating it from all other existing tools by finding the candidate regions and searching for the fusions afterwards.

Proper citation: SOAPfusion (RRID:SCR_000079) Copy   

•   Source: SciCrunch Registry

http://www.iuphar.org/

Voluntary, non-governmental, non-profit pharmacologist association promoting international cooperation, sponsoring international and regional activities, encouraging free exchange of scientists and ideas, developing public awareness, establishing advisory committees. Has official relations with the World Health Organization (WHO). Helps pharmacologists to participate with other branches of science in international activities, either directly or under ICSU, WHO and UNESCO. Member of the International Council for Science (ICSU) and participates in the work of its scientific committees. Has its own publishing program. Pharmacology International, is published every June and December. Member Directory is maintained continually, as an online resource. Provides IUPHAR Receptor Database, major on-line repository of characterization data for receptors and drugs, and the IUPHAR Ion Channels Database. Official Reports from The IUPHAR Committee on Receptor Nomenclature and Drug Classification are published in Pharmacological Reviews. IUPHAR World Congresses of Pharmacology are held every few years.

Proper citation: International Union of Basic and Clinical Pharmacology (RRID:SCR_000135) Copy   

•   Source: SciCrunch Registry

http://www.bzip.org/

A data compressor for files. This software is freely available, patent free, and is organized as a library with a programming interface.

Proper citation: bzip2 (RRID:SCR_000376) Copy   

•   Source: SciCrunch Registry

https://github.com/zhenzonglei/abat

Software stores mutiple MATLAB functions to read, analyze, and visualize various kinds of data from Allen Brain Atlas.

Proper citation: Allen Brain Atlas Tools (RRID:SCR_023855) Copy   

•   Source: SciCrunch Registry

https://www.cernerenviza.com/syndicated-insights-and-reports-for-life-sciences/cancermpact

American healthcare company that provides data, analytics, and research to the life sciences industry, with particular focus on oncology and rare diseases.

Proper citation: Cerner Enviza (RRID:SCR_024435) Copy   

•   Source: SciCrunch Registry