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http://www.canvasgfx.com/en/products/canvas-15

Illustration and communication software for engineers and technical graphics professionals that combines the ability to make 3D images while also applying filters and duatone images. The software has minimum precision levels and object illustration and image editing tools to keep data accurate throughout the authoring process. Users can accelerate and streamline the technical illustration workflow from initial import and design to final presentation, facilitate collaboration, and improve the overall productivity. Tutorials and technical documents are available on the website.

Proper citation: Canvas X (RRID:SCR_014288) Copy   

•   Source: SciCrunch Registry
  

http://www.agriculturalsoftwareconsultants.com/mixitwin

Professional feed formulation software for Windows 10 and Macs by Agricultural Software Consultants Inc. Complete feed formulation solution for professional nutritionists and feed producers. Software offers ingredient databases for various domesticated and wild species.

Proper citation: MixitWin (RRID:SCR_017553) Copy   

•   Source: SciCrunch Registry
  

https://github.com/lufuhao/HomoeologPrimer

Software tool as script used to design primers for homoeologs, to amplify either homoeolog specific or all homoeologs.

Proper citation: HomoeologPrimer (RRID:SCR_017559) Copy   

•   Source: SciCrunch Registry
  

https://europepmc.org/annotations

Text mining tool from Europe PMC that allows biological terms or concepts to be highlighted for readers on full text articles. These terms and concepts are identified by text mining algorithms, which are developed by a variety of text mining groups. However, it is up to the reader to control which selection of highlighted concepts they see. Once concepts of interest have been identified within the text, they are formatted according to the W3C Web Annotation Data Model and stored in a triple store via the EMBL-EBI RDF Platform. As a reader views an article in a web browser, any annotations in the triple store associated with the article are made available in a menu alongside the article.

Proper citation: SciLite (RRID:SCR_015015) Copy   

•   Source: SciCrunch Registry
  

https://github.com/ChristophRau/wMICA

Weighted implementation of Maximal Information Component Analysis, a co-expression network analysis algorithm for analysis of large interconnected networks and the identification of modules of similarly-acting nodes within the larger network.

Proper citation: wMICA (RRID:SCR_015490) Copy   

•   Source: SciCrunch Registry
  

http://www.inteligand.com/ligandscout/

Software that takes a macromolecular structure containing a bound ligand and identifies the key features on the ligand which are interacting with points on a protein. Its features include: automatic interpretation of PDB ligands using geometry, dictionaries and rule; advanced handling of co-factors, ions, water molecules and covalently bound ligands; pharmacophore export to Catalyst(tm), MOE(tm) and PHASE(tm) for virtual screening; and the ability to treat co-factors and water molecules as part of the ligand or part of the macromolecule.

Proper citation: LigandScout (RRID:SCR_014889) Copy   

•   Source: SciCrunch Registry
  

https://neurophysics.ucsd.edu/software.php

Matlab-based routines for the detection and clustering of putative single units from a multi-unit time series, along with quality metrics. This sofwtare was developed by the David Kleinfeld Laboratory at UC San Diego.

Proper citation: UltraMegaSort 2000 (RRID:SCR_015857) Copy   

•   Source: SciCrunch Registry
  

https://github.com/emsweene/SuBLIME_package

Software used for detection of lesions in patients with multiple sclerosis. It provides an automated method for segmenting incident lesion voxels and allows for sensitive and specific detection of lesion incidence that can be applied to large collections of images. Using the explicit form of the statistical model, SuBLIME can be adapted to cases when more or fewer imaging sequences are available.

Proper citation: SuBLIME (RRID:SCR_014409) Copy   

•   Source: SciCrunch Registry
  

https://www.charmm.org/charmm/?CFID=66837e22-4ee5-47ba-bcbf-b4b385c2397e&CFTOKEN=0

Software program that simulates molecular interactions. It has features that allow broad application to many-particle systems with a comprehensive set of energy functions, a variety of enhanced sampling methods, and support for multi-scale techniques, and a range of implicit solvent models. It also primarily targets biological systems including peptides, proteins, prosthetic groups, small molecule ligands, nucleic acids, lipids, and carbohydrates, as they occur in solution, crystals, and membrane environments. CHARMM can also be applied to inorganic materials with applications in materials design and has a comprehensive set of analysis and model builiding tools.

Proper citation: CHARMM (RRID:SCR_014892) Copy   

•   Source: SciCrunch Registry
  

https://github.com/ABCD-STUDY/FINDTHECAT

Software that conducts a jspsych test for response time evaluation. Used in the ABCD Study.

Proper citation: FINDTHECAT (RRID:SCR_016036) Copy   

•   Source: SciCrunch Registry
  

http://gaussian.com/

Software program for electronic structure modeling that enables researchers to study and predict the properties of molecules and reactions under a wide range of conditions, especially those that are difficult or impossible to observe experimentally.

Proper citation: Gaussian (RRID:SCR_014897) Copy   

•   Source: SciCrunch Registry
  

https://www.schrodinger.com/Jaguar

Ab initio molecular modeling software program that computes an array of molecular properties such as multipole moments, polarizabilities, and electrostatic potential. It can also map reaction coordinates between reactants, products, and transition states.

Proper citation: Jaguar (RRID:SCR_014895) Copy   

•   Source: SciCrunch Registry
  

https://github.com/ebtrexler/NetSuite

Software for dynamic clamping. It uses National Instruments Boards.

Proper citation: NetClamp (RRID:SCR_016275) Copy   

•   Source: SciCrunch Registry
  

https://github.com/ABCD-STUDY/stroop-task

Software that conducts the Stroop Color Task. Used in the ABCD Study.

Proper citation: stroop-task (RRID:SCR_016033) Copy   

•   Source: SciCrunch Registry
  

https://github.com/MicrosoftGenomics/FaST-LMM

FaST-LMM (Factored Spectrally Transformed Linear Mixed Models) is a set of tools for efficiently performing genome-wide association studies (GWAS), prediction, and heritability estimation on large data sets.

Proper citation: FaST LMM (RRID:SCR_015506) Copy   

•   Source: SciCrunch Registry
  

http://bioinformatics.org/ghemical/ghemical/index.html

Molecular modelling software package with 3D-visualization tools. It supports methods based on both molecular mechanics and quantum mechanics (using MOPAC7, and MPQC for QM). It contains geometry optimization (for MM and QM) and molecular dynamics (for MM) algorithms.

Proper citation: Ghemical (RRID:SCR_014899) Copy   

•   Source: SciCrunch Registry
  

https://cran.r-project.org/web/packages/devtools/index.html

Software tools to make developing R packages easier by providing R functions that simplify and expedite common tasks.

Proper citation: devtools (RRID:SCR_016961) Copy   

•   Source: SciCrunch Registry
  

https://github.com/lufuhao/ReadCleaner4Scaffolding

This pipeline and the included scripts are used to filter useful reads for SSPACE.

Proper citation: ReadCleaner4Scaffolding (RRID:SCR_016166) Copy   

•   Source: SciCrunch Registry
  

http://users.sussex.ac.uk/~lionelb/MVGC/

Matlab software toolkit designed to facilitate Granger-causal analysis with multivariate and possibly multi-trial time series data. Annotated demonstration scripts are available which may be used as templates to assist in this the toolbox's functions.

Proper citation: MVGC Multivariate Granger Causality Matlab Toolbox (RRID:SCR_015755) Copy   

•   Source: SciCrunch Registry
  

https://github.com/EpistasisLab/ReBATE

Open source software Python package to compare relief based feature selection algorithms used in data mining. Used for feature selection in any bioinformatics problem with potentially predictive features and target outcome variable, to detect feature interactions without examination of all feature combinations, to detect features involved in heterogeneous patterns of association such as genetic heterogeneity .

Proper citation: ReBATE (RRID:SCR_017139) Copy   

•   Source: SciCrunch Registry