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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   

•   Source: SciCrunch Registry
  

https://www.hpcwire.com/2005/10/28/swami_the_next_generation_biology_workbench/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. The Next Generation Biology Workbench is a free resource for research and education in Bioinformatics, Genomics, Proteomics, and Phylogenetics. The NGBW is a re-engineering of the Biology Workbench which was designed by Shankar Subramaniam and his group to provide an integrated environment where tools, user data, and public data resources can be easily accessed. The NGBW is designed to be an organic tool that evolves with the needs of the Biomedical research and education communities. The Next Generation Biology Workbench (NGBW) is now available for public use, in its production release.

Proper citation: Swami: The Next Generation Biology Workbench (RRID:SCR_007217) Copy   

•   Source: SciCrunch Registry
  

http://www.mcell.cnl.salk.edu/

Software modeling tool for realistic simulation of cellular signaling in complex 3-D subcellular microenvironment in and around living cells. Program that uses spatially realistic 3D cellular models and specialized Monte Carlo algorithms to simulate movements and reactions of molecules within and between cells.

Proper citation: MCell (RRID:SCR_007307) Copy   

•   Source: SciCrunch Registry
  

https://www.mc.vanderbilt.edu/victr/dcc/projects/acc/index.php/Main_Page

A national consortium formed to develop, disseminate, and apply approaches to research that combine DNA biorepositories with electronic medical record (EMR) systems for large-scale, high-throughput genetic research. The consortium is composed of seven member sites exploring the ability and feasibility of using EMR systems to investigate gene-disease relationships. Themes of bioinformatics, genomic medicine, privacy and community engagement are of particular relevance to eMERGE. The consortium uses data from the EMR clinical systems that represent actual health care events and focuses on ethical issues such as privacy, confidentiality, and interactions with the broader community.

Proper citation: eMERGE Network: electronic Medical Records and Genomics (RRID:SCR_007428) Copy   

•   Source: SciCrunch Registry
  

http://itools.loni.usc.edu/

An infrastructure for managing of diverse computational biology resources - data, software tools and web-services. The iTools design, implementation and meta-data content reflect the broad NCBC needs and expertise (www.NCBCs.org).

Proper citation: iTools (RRID:SCR_009626) Copy   

•   Source: SciCrunch Registry
  

http://weblogo.berkeley.edu

Web application to generate sequence logos, graphical representations of patterns within multiple sequence alignment. Designed to make generation of sequence logos easy. Sequence logo generator.

Proper citation: WEBLOGO (RRID:SCR_010236) Copy   

•   Source: SciCrunch Registry
  

http://homer.ucsd.edu/

Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++.

Proper citation: HOMER (RRID:SCR_010881) Copy   

•   Source: SciCrunch Registry
  

https://www.crisprscan.org/

Web tool for predictive sgRNA-scoring that captures sequence features affecting Cas9/sgRNA activity in vivo. Scoring algorithm to help select the best gRNAs for CRISPR.

Proper citation: CRISPRscan (RRID:SCR_023777) Copy   

•   Source: SciCrunch Registry
  

https://pathvisio.org/

Software visualization tool for biological pathways. Pathway analysis and drawing software which allows drawing, editing, and analyzing biological pathways. Developed in Java and can be extended with plugins.

Proper citation: PathVisio (RRID:SCR_023789) Copy   

•   Source: SciCrunch Registry
  

https://webprotege.stanford.edu

Web based platform for editing biomedical ontologies. Web application for editing OWL 2 ontologies. Open source, lightweight, web based ontology editor implemented in Java and JavaScript using OWL API and Google Web Toolkit. For users who do not wish to host their ontologies on Stanford servers, WebProtégé is available as Web app that can be run locally using Servlet container such as Tomcat.

Proper citation: WebProtege (RRID:SCR_024627) Copy   

•   Source: SciCrunch Registry
  

https://github.com/katiasmirn/PERFect#perfect-permutation-filtering-package-in-r

Software R package as filtering test for microbiome data. Permutation filtering approach to address two unsolved problems in microbiome data processing: (i) define and quantify loss due to filtering by implementing thresholds and (ii) introduce and evaluate a permutation test for filtering loss to provide a measure of excessive filtering.

Proper citation: PERFect (RRID:SCR_024682) Copy   

•   Source: SciCrunch Registry
  

http://drugdesigndata.org

Project portal's database of protein-ligand data sets provided by pharmaceutical partners that provide atomic details of drug mechanisms that will be used to improve computer-aided drug-design methods and thus accelerate drug discovery. The project aims to help companies release the high-quality data they have generated, which has incredible value to researchers working to improve methods of computer-aided drug discovery. Everyone stands to benefit from the ability to develop new medications more quickly and inexpensively. What computational chemists globally are trying to do is to make faster, more accurate, more predictive programs to speed up the process. Part of their mission is to engage the community in these challenges to test newly developed predictive algorithms.

Proper citation: Drug Design Data Resource (RRID:SCR_000497) Copy   

•   Source: SciCrunch Registry
  

https://openmm.org/

Software toolkit to run modern molecular simulations. It can be used either as a standalone application for running simulations, or as a library that enables accelerated calculations for molecular dynamics on high-performance computer architectures.

Proper citation: OpenMM (RRID:SCR_000436) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/apps/mediawiki/mummergpu/index.php?title=MUMmerGPU

Software tool as high throughput DNA sequence alignment program that runs on nVidia G80-class GPUs. Aligns sequences in parallel on video card to accelerate widely used serial CPU program MUMmer.

Proper citation: MUMmerGPU (RRID:SCR_001200) Copy   

•   Source: SciCrunch Registry
  

http://ccr.coriell.org/Sections/Collections/NIGMS/?SsId=8

Highly characterized cell lines and high quality DNA for cell and genetic research representing a variety of disease states, chromosomal abnormalities, apparently healthy individuals and many distinct human populations. The NIGMS Repository contains more than 10,600 cell lines, primarily fibroblasts and transformed lymphoblasts, and over 5,500 DNA samples. The NIGMS Repository has a major emphasis on heritable diseases and chromosomally aberrant cell lines. In addition, it contains a large collection dedicated to understanding human variation that includes samples from populations around the world, the CEPH collection, the Polymorphism Discovery Resource, and many apparently healthy controls. Human induced pluripotent stem cell lines, many of which were derived from NIGMS Repository fibroblasts, have recently become available through the NIGMS Repository. Sample donation facilitates all areas of research by making available well-characterized materials to any qualified researcher who might have otherwise been unable to invest the time and resources to collect needed samples independently. Donations to the Repository have created a resource of unparalleled scope. Samples from the collection have been used in more than 5,500 publications and are distributed to scientists in more than 50 countries. This resource is continuously expanding to support new directions in human genetics.

Proper citation: NIGMS Human Genetic Cell Repository (RRID:SCR_004517) Copy   

•   Source: SciCrunch Registry
  

http://wikipathways.org/

Open and collaborative platform dedicated to curation of biological pathways. Each pathway has dedicated wiki page, displaying current diagram, description, references, download options, version history, and component gene and protein lists. Database of biological pathways maintained by and for scientific community.

Proper citation: WikiPathways (RRID:SCR_002134) Copy   

•   Source: SciCrunch Registry
  

https://sites.google.com/site/friaptamerstream/

The Aptamer Database is a comprehensive, annotated repository for information about aptamers and in vitro selection. This resource is provided to collect, organize and distribute all the known information regarding aptamer selection. Aptamers are DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules. Aptamers have been selected which bind nucleic acid, proteins, small organic compounds, and even entire organisms.

Proper citation: Aptamer Database - The Ellington Lab (RRID:SCR_001781) Copy   

•   Source: SciCrunch Registry
  

http://www.uniprot.org/

Collection of data of protein sequence and functional information. Resource for protein sequence and annotation data. Consortium for preservation of the UniProt databases: UniProt Knowledgebase (UniProtKB), UniProt Reference Clusters (UniRef), and UniProt Archive (UniParc), UniProt Proteomes. Collaboration between European Bioinformatics Institute (EMBL-EBI), SIB Swiss Institute of Bioinformatics and Protein Information Resource. Swiss-Prot is a curated subset of UniProtKB.

Proper citation: UniProt (RRID:SCR_002380) Copy   

•   Source: SciCrunch Registry
  

http://bioinf-apache.charite.de/supertarget_v2/

Database for analyzing drug-target interactions, it integrates drug-related information associated with medical indications, adverse drug effects, drug metabolism, pathways and Gene Ontology (GO) terms for target proteins. At present (May 2013), the updated database contains >6000 target proteins, which are annotated with >330 000 relations to 196 000 compounds (including approved drugs); the vast majority of interactions include binding affinities and pointers to the respective literature sources. The user interface provides tools for drug screening and target similarity inclusion. A query interface enables the user to pose complex queries, for example, to find drugs that target a certain pathway, interacting drugs that are metabolized by the same cytochrome P450 or drugs that target proteins within a certain affinity range.

Proper citation: SuperTarget (RRID:SCR_002696) Copy   

•   Source: SciCrunch Registry
  

http://people.biochem.umass.edu/fournierlab/3dmodmap/

Database of maps showing the sites of modified rRNA nucleotides. Access to the rRNA sequences, secondary structures both with modification sites indicated, 3D modification maps and the supporting tables of equivalent nucleotides for rRNA from model organisms including yeast, arabidopsis, e. coli and human is provided. This database complements the Yeast snoRNA Database at UMass-Amherst and relies on linking to some content from that database, as well as to others by colleagues in related fields. Therefore, please be very cognizant as to the source when citing information obtained herein. Locations of modified rRNA nucleotides within the 3D structure of the ribosome.

Proper citation: 3D Ribosomal Modification Maps Database (RRID:SCR_003097) Copy   

•   Source: SciCrunch Registry