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http://standage.github.io/AEGeAn
Software toolkit for the analysis and evaluation of genome annotations. The toolkit includes a variety of analysis programs, e.g. for comparing distinct sets of gene structure annotations (ParsEval), computation of gene loci (LocusPocus) and more.
Proper citation: Aegean (RRID:SCR_015965) Copy
Simulation software for experimental evolution of microorganisms. Aevol is a digital genetics model for the study of structural variations of the genome (e.g. number of genes, synteny, proportion of coding sequences).
Proper citation: Aevol (RRID:SCR_015966) Copy
https://github.com/EvolBioInf/andi
Software tool for rapidly computing and estimating evolutionary distance between closely related genomes. Because andi does not compute full alignments it scales even up to thousands of bacterial genomes.
Proper citation: andi (RRID:SCR_015971) Copy
https://github.com/ABCD-STUDY/tick-tock
Software for research study observation that visualizes study related events per day. Any event generating function sends a 'tick' event to this application which will be visible on this applications web-interface.
Proper citation: tick-tock (RRID:SCR_016023) Copy
https://bioinf.eva.mpg.de/anfo/
Software for short read alignment and mapping of sequencing reads where the DNA sequence is somehow modified and/or there is more divergence between sample and reference than what fast mappers will handle.
Proper citation: Anfo (RRID:SCR_015972) Copy
https://github.com/ABCD-STUDY/FIONA-protocol-compliance
Software that contains multiple sequential lines of MATLAB commands and function calls for numerical computing for ABCD study protocol compliance.
Proper citation: FIONA-protocol-compliance (RRID:SCR_016027) Copy
https://github.com/ABCD-STUDY/Fast-Track-Image-Sharing
Software for sharing the ABCD (Adolescent Brain Cognitive Development) study data on the National Data Archive (NDA).
Proper citation: Fast-Track-Image-Sharing (RRID:SCR_016021) Copy
https://github.com/ABCD-STUDY/eprime-data-clean
Software to convert E-Prime (software tool for psychology computerized experiment design, data collection, and analysis) generated files to CSV files without errors during conversion. The ABCD project is using E-Prime to run behavioral tests.
Proper citation: eprime-data-clean (RRID:SCR_016020) Copy
THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone. Software for bacterial microscopy image analysis. It is designed to detect and outline bacterial cells in microscopy images and to analyze fluorescence signal inside them.
Proper citation: MicrobeTracker (RRID:SCR_015939) Copy
University in Durham, England.
Proper citation: Durham University; Durham; England (RRID:SCR_016079) Copy
https://github.com/harry-thorpe/piggy
Pipeline for analyzing intergenic regions in bacteria. It is designed to be used in conjunction with Roary (https://github.com/sanger-pathogens/Roary).
Proper citation: Piggy (RRID:SCR_015941) Copy
https://github.com/KravitzLab/fed/wiki
Flexible open-source device for measuring feeding behavior. FED measures food intake in mice. It is battery powered and designed to be used in rodent colony caging.Home cage-compatible feeding system that measures food intake with high accuracy and temporal resolution. FED offers alternative to commercial feeders, with convenience of use in tradition colony rack caging.
Proper citation: Feeding Experimentation Device project (RRID:SCR_015942) Copy
http://disulfind.dsi.unifi.it/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023, Software for predicting the disulfide bonding state of cysteines and their disulfide connectivity, starting from a protein sequence alone and may be useful in other genomic annotation tasks.
Proper citation: DISULFIND (RRID:SCR_016072) Copy
https://github.com/boutiques/boutiques/
Software toolkit for a cross-platform JSON-framework for describing command-line tools and their parameters. It is accompanied by a Python tool which facilitates the creation, validation, simulation, execution, publishing, evaluation, and testing of tools described in this format.
Proper citation: Boutiques (RRID:SCR_016073) Copy
https://bitbucket.org/vboza/deepnano
Software for an alternative basecaller for DNA base calling in the portable Oxford Nanopore MinION sequencing device, based on deep recurrent neural networks. Used to improve base calling accuracy and reduce sequencing error rate.
Proper citation: DeepNano (RRID:SCR_016070) Copy
Statistical software that provides classes and functions for the estimation of many different models, as well as for conducting statistical tests, and statistical data exploration. The results are tested against existing statistical packages to ensure that they are correct. http://conference.scipy.org/proceedings/scipy2010/seabold.html
Proper citation: statsmodel (RRID:SCR_016074) Copy
http://molevol.cmima.csic.es/castresana/Gblocks_server.html
Software that eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Gblocks (RRID:SCR_015945) Copy
Visualization software that links unique leaf labels to lists of variables/values pairs of annotations (meta-information), independently of the tree topologies, remaining fully compatible with the basic newick format. These relationships are used by dynamic graphics operators, information visualization methods like Projection, Localization, Labelization, Reflection allowing an interaction from annotations to trees, from trees to annotations and from trees to trees through annotations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: TreeDyn (RRID:SCR_015946) Copy
Software for a measurement and control system for behavior research, most often used to implement operant (Go/NoGo, 2AFC) tasks. This software controls a hierarchy of hardware modules, each powered by an Arduino-programmable microcontroller.
Proper citation: Bpod (RRID:SCR_015943) Copy
http://www.genetherapyreview.com/gene-therapy-research
The National Gene Vector Laboratories (NGVL) was established as a cooperative national effort to produce and distribute vectors for human gene transfer studies.
Proper citation: National Gene Vector Laboratories (RRID:SCR_015944) Copy
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