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http://contra.stanford.edu/contrafold/

Software novel secondary structure prediction method based on conditional log-linear models, a flexible class of probabilistic models which generalize upon SCFGs by using discriminative training and feature-rich scoring. Used for sequence prediction.

Proper citation: CONTRAfold (RRID:SCR_023994) Copy   

•   Source: SciCrunch Registry

https://github.com/bioinfo-center-pasteur-fr/toppred

Software tool for membrane protein structure prediction.Transmembrane topology prediction.Used for predicting topology of bacterial inner membrane proteins.

Proper citation: toppred (RRID:SCR_024385) Copy   

•   Source: SciCrunch Registry

https://github.com/paulgeeleher/pRRophetic

Software R package for prediction of clinical chemotherapeutic response from tumor gene expression levels. Used to predict phenotypes from gene expression microarray data, gene expression microarray data,

Proper citation: pRRophetic (RRID:SCR_024417) Copy   

•   Source: SciCrunch Registry

https://rostlab.org/owiki/index.php/Metastudent

Software tool to predict gene ontology terms for protein sequences through homology.

Proper citation: Metastudent (RRID:SCR_024110) Copy   

•   Source: SciCrunch Registry

https://github.com/bartongroup/yanosim

Software tool as read simulator for nanopore DRS datasets.

Proper citation: Yanosim (RRID:SCR_024363) Copy   

•   Source: SciCrunch Registry

http://www.ctsim.org

Software tool to simulate process of transmitting X-rays through phantom objects. Reconstructs original phantom image from projections. Has wide array of image analysis and image processing functions.

Proper citation: CTSim (RRID:SCR_024004) Copy   

•   Source: SciCrunch Registry

https://cab.spbu.ru/software/spades/

Software package for assembling single cell genomes and mini metagenomes. Uses short read sets as input. Used for genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. Works with Illumina or IonTorrent reads and can provide hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Intended for small genomes like bacterial or fungal., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SPAdes (RRID:SCR_000131) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/DrugSim2DR/

Software R package to predict drug functional similarity to drug repurposing.

Proper citation: DrugSim2DR (RRID:SCR_024564) Copy   

•   Source: SciCrunch Registry

http://www.jsps.go.jp/english/

Research and outreach organization dedicated to promoting science, research and education. The society has four main objectives, including building international cooperative networks, enhancing education and research at universities, building evidence-based science-promotion systems and creating diverse world level knowledge.

Proper citation: Japan Society for the Promotion of Science (RRID:SCR_001085) Copy   

•   Source: SciCrunch Registry

https://github.com/chaoszhang/A-pro

Software tool for species tree reconstruction from multi-copy gene family trees.Used for estimating unrooted species tree given set of unrooted gene trees and is statistically consistent under the multi-species coalescent model. ASTRAL-pro extends ASTRAL to allow multi-copy genes. ASTRAL-Pro 2, ultrafast and memory efficient version of ASTRAL-Pro that adopts placement based optimization algorithm for significantly better scalability without sacrificing accuracy.

Proper citation: ASTRAL-Pro (RRID:SCR_024520) Copy   

•   Source: SciCrunch Registry

http://mindboggle.info/data.html

Complete set of free, publicly accessible, downloadable atlases, templates, and individual manually labeled brain image data, the largest collection of publicly available, manually labeled human brains in the world! http://journal.frontiersin.org/article/10.3389/fnins.2012.00171/full

Proper citation: Mindboggle-101 atlases (RRID:SCR_002439) Copy   

•   Source: SciCrunch Registry

http://www.openlinksw.com/

An technology innovator in database and application server software that has been a long time developer of database and semantic repository technologies on both single servers and clusters. This, combined with OpenLink's experience with SQL, gives an all round view of performance across many environments and workload profiles, from transactions to decision support or search. OpenLink also has extensive experience in developing scale-out parallel database technology. The cross-platform product portfolio addresses challenges such as: Universal Data Access, Data Virtualization & Management, Personal & Enterprise Data Spaces, and Implementation & Support.

Proper citation: OpenLink Software (RRID:SCR_003662) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/primate_atlas/

Symmetric atlas of the primate brain created using 18 cases of rhesus macaques aged 16-34 months. It includes the T1-weighted image (with and without skull), and also tissue segmentation probability maps (white matter, gray matter, CSF, rest), subcortical structures segmentation (amygdala, caudate, hippocampus, pallidus, putamen), and a lobar parcellation map. You can find more details about the creation of this atlas in the following paper : M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. In Proc SPIE Vol 6512, Medical Imaging, 2007, pp. 65122 L1-8

Proper citation: UNC Primate Brain Atlas (RRID:SCR_002570) Copy   

•   Source: SciCrunch Registry

http://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infant-0-1-2-atlases

3 atlases dedicated for neonates, 1-year-olds, and 2-year-olds. Each atlas comprises a set of 3D images made up of the intensity model, tissue probability maps, and anatomical parcellation map. These atlases are constructed with the help of state-of-the-art infant MR segmentation and groupwise registration methods, on a set of longitudinal images acquired from 95 normal infants (56 males and 39 females) at neonate, 1-year-old, and 2-year-old.

Proper citation: UNC Infant 0-1-2 Atlases (RRID:SCR_002569) Copy   

•   Source: SciCrunch Registry

http://www.gnubila.com/

A commercial software and service company operating in Spain, France and Colombia whose main stakeholder is Indra and its main product is the G platform, on top of which they have developed several vertical applications for various industry sectors like banking, healthcare, government and SMB. Since its constitution, gn??bila has constituted an international reference in the development and deployment of Network Service Infrastructures and Platforms for Businesses, Organizations and Individuals, facilitating communication, collaboration and the coordination of applications, data and information. gn??bila Products: * Cloud Application Platform * Cloud TP Platform * Platform as a Service * Development Platform

Proper citation: Gnubila (RRID:SCR_004109) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/saibn/

A 3D stereoscopic (anaglyph method) full brain functional connectivity atlas created using a parcellation atlas published by Craddock et al. (2012). Using 3D Slicer 3.6.3 and the two hundred Region of Interest (ROI) version of the Craddock atlas, 200 grayscale surface models were created using a z-stat threshold > 2.3, and each surface model was processed with a surface decimation algorithm, smoothed with the Taubin algorithm and without surface normals. For improved visualization of the functional connectivity networks and their relative anatomical position, the surface model of five subcortical anatomical structures (corpus callosum, bilateral caudate, pallidum, putamen, thalamus, amygdala and hippocampus) were included in SAIBN. These surfaces were created with 3D Slicer using the segmentation computed with Freesurfer v. 5.1. The viewer should use red-cyan glasses to see the 3D stereoscopic effect using 3D Slicer (version 3.6.3, http://www.slicer.org/pages/Special:SlicerDownloads).

Proper citation: Stereoscopic Atlas of Intrinsic Brain Networks (RRID:SCR_002568) Copy   

•   Source: SciCrunch Registry

http://www.gensat.org/retina.jsp

Collection of images from cell type-specific protein expression in retina using BAC transgenic mice. Images from cell type-specific protein expression in retina using BAC transgenic mice from GENSAT project.

Proper citation: Retina Project (RRID:SCR_002884) Copy   

•   Source: SciCrunch Registry

http://www.escholarship.org/

Provides comprehensive publication services for Univeristy of California affiliated departments, research units, publishing programs, and individual scholars who seek to publish original, open access journals, books, conference proceedings, and other scholarship. Content is delivered via research platform and is available to scholars worldwide.

Proper citation: eScholarship (RRID:SCR_002624) Copy   

•   Source: SciCrunch Registry

http://zebrafinch.brainarchitecture.org/

Atlas of high resolution Nissl stained digital images of the brain of the zebra finch, the mainstay of songbird research. The cytoarchitectural high resolution photographs and atlas presented here aim at facilitating electrode placement, connectional studies, and cytoarchitectonic analysis. This initial atlas is not in stereotaxic coordinate space. It is intended to complement the stereotaxic atlases of Akutegawa and Konishi, and that of Nixdorf and Bischof. (Akutagawa E. and Konishi M., stereotaxic atalas of the brain of zebra finch, unpublished. and Nixdorf-Bergweiler B. E. and Bischof H. J., A Stereotaxic Atlas of the Brain Of the Zebra Finch, Taeniopygia Guttata, http://www.ncbi.nlm.nih.gov.) The zebra finch has proven to be the most widely used model organism for the study of the neurological and behavioral development of birdsong. A unique strength of this research area is its integrative nature, encompassing field studies and ethologically grounded behavioral biology, as well as neurophysiological and molecular levels of analysis. The availability of dimensionally accurate and detailed atlases and photographs of the brain of male and female animals, as well as of the brain during development, can be expected to play an important role in this research program. Traditionally, atlases for the zebra finch brain have only been available in printed format, with the limitation of low image resolution of the cell stained sections. The advantages of a digital atlas over a traditional paper-based atlas are three-fold. * The digital atlas can be viewed at multiple resolutions. At low magnification, it provides an overview of brain sections and regions, while at higher magnification, it shows exquisite details of the cytoarchitectural structure. * It allows digital re-slicing of the brain. The original photographs of brain were taken in certain selected planes of section. However, the brains are seldom sliced in exactly the same plane in real experiments. Re-slicing provides a useful atlas in user-chosen planes, which are otherwise unavailable in the paper-based version. * It can be made available on the internet. High resolution histological datasets can be independently evaluated in light of new experimental anatomical, physiological and molecular studies.

Proper citation: Zebrafinch Brain Architecture Project (RRID:SCR_004277) Copy   

•   Source: SciCrunch Registry

https://reich.hms.harvard.edu/software

Software application that finds skews in ancestry that are potentially associated with disease genes in recently mixed populations like African Americans. It can be downloaded for either UNIX or Linux.

Proper citation: Ancestrymap (RRID:SCR_004353) Copy   

•   Source: SciCrunch Registry