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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
http://go.princeton.edu/cgi-bin/GOTermFinder
The Generic GO Term Finder finds the significant GO terms shared among a list of genes from an organism, displaying the results in a table and as a graph (showing the terms and their ancestry). The user may optionally provide background information or a custom gene association file or filter evidence codes. This tool is capable of batch processing multiple queries at once. GO::TermFinder comprises a set of object-oriented Perl modules GO::TermFinder can be used on any system on which Perl can be run, either as a command line application, in single or batch mode, or as a web-based CGI script. This implementation, developed at the Lewis-Sigler Institute at Princeton, depends on the GO-TermFinder software written by Gavin Sherlock and Shuai Weng at Stanford University and the GO:View module written by Shuai Weng. It is made publicly available through the GMOD project. The full source code and documentation for GO:TermFinder are freely available from http://search.cpan.org/dist/GO-TermFinder/. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Proper citation: Generic GO Term Finder (RRID:SCR_008870) Copy
A private Ivy League research university based in New Jersey that confers undergraduate and graduate degrees in the humanities, social sciences, natural sciences, and engineering. It offers professional degrees in international affairs, engineering and applied science, architecture, and finance
Proper citation: Princeton University; New Jersey; USA (RRID:SCR_001059) Copy
Welcome to CPAN, where you you will find All Things Perl. CPAN is the Comprehensive Perl Archive Network, a large collection of Perl software and documentation. You can begin exploring from either http://www.cpan.org/, http://www.perl.com/CPAN/ or any of the mirrors listed at http://www.cpan.org/SITES.html. Note that CPAN is also the name of a Perl module, CPAN.pm, which is used to download and install Perl software from the CPAN archive. This FAQ covers only a little about the CPAN module and you may find the documentation for it by using perldoc CPAN via the command line or on the web at http://search.cpan.org/dist/CPAN/lib/CPAN.pm. Sponsors: CPAN works with the generosity and cooperation of hundreds of developers, over 100 participating mirrors, funet.fi donating the network bandwidth, storage space and computing power, volunteers who help keep everything together and users whose interest in Perl keep the archive alive and growing. Keywords: Comprehension, Perl, Archive, Software, Documentation,
Proper citation: Comprehensive Perl Archive Network (RRID:SCR_007253) Copy
Computable knowledge regarding functions of genes and gene products. GO resources include biomedical ontologies that cover molecular domains of all life forms as well as extensive compilations of gene product annotations to these ontologies that provide largely species-neutral, comprehensive statements about what gene products do. Used to standardize representation of gene and gene product attributes across species and databases.
Proper citation: Gene Ontology (RRID:SCR_002811) Copy
http://geneontology.org/docs/tools-overview/
Collection of tools developed by GO Consortium and by third parties. Tools are listed by category or alphabetically and continue to be improved and expanded.
Proper citation: Gene Ontology Tools (RRID:SCR_006941) Copy
https://3dvcell.ncbi.nlm.nih.gov/
THIS RESOURCE IS NO LONGER IN SERVICE, confirmed by curator 11/21/2018; Community of researchers attempting to build a comprehensive virtual cell model. The 3DVC will do for cell biology what the Large Hadron Collider (LHC) does for particle physics, but through a virtual rather than physical resource. It will bring together collaborators around a shared infrastructure to advance the field through efficient groundbreaking science and technology, the results of which will be broadly disseminated to an audience ranging from K12 to professionals. The 3DVC is committed to open science, yet strives for sustainability through new business models that leverages that open content.
Proper citation: 3DVC (RRID:SCR_001377) Copy
http://gmod.org/wiki/Main_Page
A collection of open source software tools for creating and managing genome-scale biological databases. GMOD is made up databases, applications, and adaptor software that connects these components together. You can use it to create a small laboratory database of genome annotations, or a large web-accessible community database. At first GMOD just featured model organisms but now any organism with any kind of sequence associated with it is a good candidate as a subject for a GMOD database. There are GMOD databases with just protein sequence in them, with EST sequence only, those that are concerned primarily with gene expression, and even those dedicated to collections of RNA sequence. They have also heard of GMOD databases for oligonucleotides and plasmids.
Proper citation: Generic Model Organism Database Project (RRID:SCR_001731) Copy
Community registry of software tools and data resources for life sciences. Tools and data services registry as community effort to document bioinformatics resources. Registry of software and databases, facilitating researchers from across spectrum of biological and biomedical science. When adding tools to registry, information including URL, contact information, resource function, field its relevant in, and its primary publication are required. Development is supported by ELIXIR - the European Infrastructure for Biological Information.
Proper citation: bio.tools (RRID:SCR_014695) Copy
Debian is Linux distribution composed of free and open source software, developed by community supported Debian Project, which was established by Ian Murdock on August 16, 1993.Debian comes with over 59000 packages (precompiled software that is bundled up in nice format for easy installation on your machine), package manager (APT), and other utilities that make it possible to manage thousands of packages on thousands of computers as easily as installing single application.
Proper citation: Debian (RRID:SCR_006638) Copy
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Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
