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http://www.fujitsu.com/jp/group/kyushu/en/solutions/industry/lifescience/admeworks/
Software program for high-speed virtual screening intended for simultaneous evaluation of ADMET properties of compounds. ADMEWORKS Predictor employs a number of models to predict ADMET properties using models based on values of topological, geometric, physicochemical and substructure descriptors derived from the molecular structures.
Proper citation: ADMEWORKS Predictor (RRID:SCR_014905) Copy
http://www.optibrium.com/stardrop/index.php
Software toolkit for drug design and discovery, including plugins for in silico compound optimization, compound selection and integration into other databases.
Proper citation: StarDrop (RRID:SCR_014902) Copy
Web application which allows users to visualise and collaboratively segment and annotate any brain MRI dataset available online via URL. A list of brains are available for use on the main site. Segmentations are automatically saved and can be downloaded as Nifti files or triangular meshes. Users can point BrainBox to their own Nifti data, or try data catalogues created by the community.
Proper citation: BrainBox (RRID:SCR_014750) Copy
http://www.moldiscovery.com/software/vsplus/
Software package for molecular descriptors, ADME prediction and membrane permeability prediction. These can then be used with provided chemometric tools to build statistical models.
Proper citation: VolSurf (RRID:SCR_014911) Copy
http://www.bio-rad.com/en-us/sku/soft-om-sw-opticon-monitor-software
Software which controls all operations in the experimental setup, data acquisition and monitoring, and data analysis stages of the Bio-Rad Opticon 2 system. In the experimental setup stage, setup and programming operations are accessed from the Master File window. The master file consists of a plate file, which specifies the parameters of the plate, and a protocol file, which specifies the experimental conditions. After a plate and a protocol setup have been created or selected, a run can be initiated, which begins the data acquisition and monitoring stage. Data collection can be monitored during the run by viewing a plot of fluorescence intensity vs. cycle number. In the data analysis stage, data can be analyzed using the Quantitation, Melting Curve, and/or Analysis windows. The window used depends on the type of data being collected.
Proper citation: Opticon Monitor Software (RRID:SCR_014241) Copy
A software application which provides feedback on writing, wording, and frequency of text by checking against databases of correct language. Users can highlight a chunk of text and use Writefull to see how often the specific text appears in different language databases. Writefull can also offer synonyms and suggestions for wording. Writefull is supported by numerous writing tools which include MS Word and Gmail.
Proper citation: Writefull (RRID:SCR_014006) Copy
A GDS and OASIS file viewer editor that has file overlay and file creation capabilities. It features include: layer grouping, flexible rulers, image overlay, partial editing functions, and external library support.
Proper citation: KLayout (RRID:SCR_014644) Copy
http://www.ccp4.ac.uk/html/pointless.html
Pointless scores all the possible Laue groups consistent with the crystal class, which is based on cell dimension restraints, by matching potential symmetry equivalent reflections. For chiral systems, the Laue group uniquely implies the point group then checks sets of reflections which may be systematically absent to suggest a possible spacegroup. There is also a check for lattice centering, i.e., a check for whole classes of reflections having essentially zero intensity, including a check for obverse/inverse twinning in rhombohedral systems. Pointless is also capable of converting XDS, Scalepack, SHELX or SAINT formats to MTZ.
Proper citation: Pointless (RRID:SCR_014218) Copy
http://www.nitrc.org/projects/dti-denoising/
A Matlab package which contains six denoising filters and a noise estimation method for 4D DWI. The package includes nonlocal means, local PCA and Oracle DCT methods. Based on image redundancy and/or sparsity, the proposed filters provide efficient denoising while preserving fine structures.
Proper citation: DTI denoising (RRID:SCR_014102) Copy
https://github.com/missy139/PreSurgMapp
A MATLAB toolbox for processing the functional areas of the brain using multi-modal fMRI data for pre-surgical mapping. It is composed of three types of individual-level ICA analyses for user use. Traditional ICA (task) can be used for task fMRI. Either Traditional ICA (rest) or ICA with DICI (rest) can be used for rs-fMRI. Traditional ICA (rest) is designed for users who already have a hypothesis of the pattern of the target component and want to have manually set components by themselves. ICA with DICI (rest) is completely automatic, given that the user provides a template (provided). The software utilizes an automatic component identification method that is based on the discriminatory-index. All the components from multiple ICA runs with multiple component settings are ranked and compiled.
Proper citation: PreSurgMapp (RRID:SCR_014427) Copy
An open-source cheminformatics and machine-learning toolkit that is useable from Java or Python. It includes a collection of standard cheminformatics functionality for molecule I/O, substructure searching, chemical reactions, coordinate generation (2D or 3D), fingerprinting, etc., as well as a high-performance database cartridge for working with molecules using the PostgreSQL database. Documentation is available on the main website.
Proper citation: RDKit: Open-Source Cheminformatics Software (RRID:SCR_014274) Copy
A multi-purpose project automation tool written in Python which helps create technical documents. Dexy is a free-form literate documentation tool for writing any kind of technical document incorporating code. It provides a consistent interface to tools and scripts and keeps track of what to run, in which order, and with what parameters.
Proper citation: Dexy (RRID:SCR_013982) Copy
A package of over twenty mass spectrometry-based tools primarily geared toward proteomic data analysis and database mining. It can be run from the command line, but is primarily used through a web browser, and there is a public website that allows anyone to use the software without local installation. Tandem mass spectrometry analysis tools are used for database searching and identification of peptides, including post-translationally modified peptides and cross-linked peptides. Support for isotope and label-free quantification from this type of data is provided. MS-Viewer software allows sharing and displaying of annotated spectra from many different tandem mass spectrometry data analysis packages. Other tools include software for analyzing peptide mass fingerprinting data (MS-Fit); prediction of theoretical fragmentation of peptides (MS-Product); theoretical chemical or enzymatic digestion of proteins (MS-Digest); and theoretical modeling of the isotope distribution of any chemical, including peptides (MS-Isotope). Searches using amino acid sequence can be used to identify homologous peptides in a database (MS-Pattern); the use of the combination of amino acid sequence and masses can be used for homologous peptide and protein identification using MS-Homology. Tandem mass spectrometry peak list files can be filtered for the presence of certain peaks or neutral losses using MS-Filter. Given a list of proteins, MS-Bridge can report all potential cross-linked peptide combinations of a specified mass. Given a precursor peptide mass and information about known amino acid presence, absence, or modifications, MS-Comp can report all amino acid combinations that could lead to the observed mass.
Proper citation: Protein Prospector (RRID:SCR_014558) Copy
http://www.acdlabs.com/resources/freeware/nmr_proc/
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 27, 2016. A software package that provides 1D and 2D NMR tools as well as processing and interpretation for all other major analytical techniques (LC/MS, IR, Raman, and more) in one package. It also has support for structure verification and multiplet reports.
Proper citation: ACD/ NMR Processor (RRID:SCR_014679) Copy
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
https://www.omicron-laser.de/english/lasers/diode-lasers/phoxx-lasers/phoxx-diode-laser.html
Software application for PhoxX® Diode Laser to support Omicron products. It is related to uManager open source microscopy software for control of microscopes.
Proper citation: PhoxX Controller (RRID:SCR_016309) Copy
https://www.axionbiosystems.com/products/axis-software
Software for multi electrode array recording for Axion Biosystems. Used in enhancing cardiac and neural analysis through data processing and signal monitoring.
Proper citation: AxIS (RRID:SCR_016308) Copy
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
https://github.com/ebtrexler/NetSuite
Software for dynamic clamping. It uses National Instruments Boards.
Proper citation: NetClamp (RRID:SCR_016275) Copy
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
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