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Portal enables browsing, searching, and analysis of human genetic and genomic information linked to musculoskeletal traits and diseases, while protecting the integrity and confidentiality of underlying data.
Proper citation: Musculoskeletal Knowledge Portal (RRID:SCR_023171) Copy
https://github.com/CompSynBioLab-KoreaUniv/FunGAP
Software tool to predict protein coding genes in fungal genome assembly. Performs gene prediction on given genome assembly and RNA-seq reads. Runs multiple gene predictors, evaluates all predicted genes, and assembles gene models that are highly supported by homology to known sequences.
Proper citation: FunGAP (RRID:SCR_023213) Copy
Clinical research platform and longitudinal observational study for Huntington’s Disease families intended to accelerate progress towards therapeutics. Collaboration between Huntington’s disease families, clinicians, and researchers to accelerate progress toward effective treatments.
Proper citation: Enroll-HD (RRID:SCR_023300) Copy
https://github.com/saeyslab/nichenetr
Software tool as R implementation of NicheNet method to predict active ligand-target links between interacting cells. NicheNet uses human or mouse gene expression data of interacting cells as input and combines this with prior model that integrates existing knowledge on ligand-to-target signaling paths. This allows to predict ligand-receptor interactions that might drive gene expression changes in cells of interest.
Proper citation: NicheNet (RRID:SCR_023158) Copy
https://rostlab.org/owiki/index.php/PROFisis
Software tool that identifies interacting residues from sequence alone. Developed using transient protein�protein interfaces from complexes of experimentally known 3D structures.
Proper citation: PROFisis (RRID:SCR_024179) Copy
Software for managing geochemical data created by individual geochronology laboratory. Designed for flexibility and extensibility, so that it can be tailored to the needs of individual analytical labs that manage wide variety of data. Database set up for metadata tracking.
Proper citation: Sparrow-data (RRID:SCR_024432) Copy
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
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
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
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
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
https://github.com/bartongroup/yanosim
Software tool as read simulator for nanopore DRS datasets.
Proper citation: Yanosim (RRID:SCR_024363) Copy
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
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
https://github.com/cortex-lab/Rigbox
Open source software MATLAB toolbox for running behavioral neuroscience experiments and managing data.Used for probing neurons and behavior. Used for managing behavioral neuroscience experiments and acquiring experiment related data.
Proper citation: Rigbox (RRID:SCR_021517) Copy
Portal that provides multimedia educational content from courses, conference lectures, and laboratory exercises from some of leading neuroscience institutes and societies to be more accessible to global neuroscience community.
Proper citation: TrainingSpace (RRID:SCR_022036) Copy
Software tool as biophysical simulation model for livestock systems. It has flexible interface for setting up and running simulations with extensive graphical and data output.
Proper citation: Sustainable Grazing System Pasture Model (RRID:SCR_021854) Copy
https://www.research.va.gov/mvp/
National research program to learn how genes, lifestyle, and military exposures affect health and illness.
Proper citation: Million Veteran Program (RRID:SCR_021731) Copy
Software allows estimating growth and production at stand level of main forest species implanted in Argentine Mesopotamia such as Pino taeda, Eucalyptus grandis, Pino elliottii and Araucaria angustifolia. Areas for which models were adjusted correspond to province of Misiones, northeast of Corrientes and Concordia in province of Entre Ríos.
Proper citation: PlaForNEA (RRID:SCR_022027) Copy
https://simulabeta.sourceforge.io/
Software tool as simulation program for insulin glucose feedback control. Based on nonlinear MiMe-NoCoDI model.
Proper citation: SimulaBeta (RRID:SCR_021900) Copy
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