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http://owlapi.sourceforge.net/
The OWL API is a Java API and reference implementation for creating, manipulating and serializing OWL Ontologies. The latest version of the API is focused towards OWL 2. The OWLAPI underpins ontology browsing and editing tools and platforms such as SWOOP and Protege4. Note that this API, or any other OWL-based API, can be used without an integrated OWL parser if you download a pre-converted OWL file generated from OBO. See OBO Ontologies List for all OBO ontologies converted to OWL (we do not list the full complement of OWL-based APIs here, only those of direct relevance to GO). The OWL API includes the following components: * An API for OWL 2 and an efficient in-memory reference implementation * RDF/XML parser and writer * OWL/XML parser and writer * OWL Functional Syntax parser and writer * Turtle parser and writer * KRSS parser * OBO Flat file format parser * Reasoner interfaces for working with reasoners such as FaCT++, HermiT, Pellet and Racer Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible
Proper citation: OWL API (RRID:SCR_005734) Copy
http://neurofitter.sourceforge.net
Neurofitter is software for parameter tuning of electrophysiological neuron models. It automatically searches for sets of parameters of neuron models that best fit available experimental data, and therefore acts as an interface between neuron simulators, like Neuron or Genesis, and optimization algorithms, like Particle Swarm Optimization, Evolutionary Strategies, etc.
Proper citation: Neurofitter (RRID:SCR_005843) Copy
OrChem is an extension for the Oracle 11G database that adds registration and indexing of chemical structures to support fast substructure and similarity searching. The cheminformatics functionality is provided by the Chemistry Development Kit. OrChem provides similarity searching with response times in the order of seconds for databases with millions of compounds, depending on a given similarity cut-off. For substructure searching, it can make use of multiple processor cores on today''s powerful database servers to provide fast response times in equally large data sets. OrChem is an Oracle chemistry plug-in using the Chemistry Development Kit (CDK). The CDK is an open source Java library for Chemoinformatics and Bioinformatics. OrChem is maintained by the chemoinformatics and metabolism team of the European Bioinformatics Institute. Oracle Data cartridges extend the capabilities of the Oracle server. For chemistry various commercial cartridges exist that facilitate searching and analyzing chemical data. OrChem also provides functionality like this, but is not a cartridge. It doesn''t need Oracle''s extensibility architecture because its Java components run as Java stored procedures inside the Oracle standard JVM (Aurora). OrChem is suitable for Oracle 11G and onwards. Starting with Oracle 11g release 1 (11.1) there is a just-in-time(JIT) compiler for Oracle JVM environment. A JIT compiler for Oracle JVM enables much faster execution because it manages the invalidation, recompilation, and storage of code without an external mechanism. This new Oracle feature makes Java classes perform better than before.
Proper citation: OrChem (RRID:SCR_008865) Copy
http://sccn.ucsd.edu/wiki/BCILAB
Open Source MATLAB toolbox and EEGLAB plugin for the design, prototyping, testing, experimentation with, and evaluation of Brain-Computer Interfaces (BCIs), and other systems in the same computational framework. It facilitates the design and development of new methods for cognitive state estimation and their use in both offline data analysis and real-time applications. BCILAB includes an easily extensible collection of currently over 100 methods from the literature (covering signal processing, machine learning and BCI-specific methods). Aside from supporting advanced BCI research, a special aim of BCILAB is to facilitate the adoption of machine learning and advanced statistical modeling for functional neuroimaging purposes in tandem with the EEGLAB platform. The toolbox offers multiple different interfaces which link to the same backend functionality, including a GUI, scripting support (MATLAB-based), APIs for real-time processing, and a variety of extension component interfaces. MATLAB programming is not strictly necessary, as most BCILAB features can be accessed from the GUI, although it is required for batch scripting and custom extensions. The strength of MATLAB-based software lies in its resources for leading-edge scientific computing, as well as in the good support for rapid prototyping, but BCI systems developed in it can be used for real-time out-of-lab experimentation, and can in principle be deployed without the need for a MATLAB license. However, due to the complexity and overhead of the MATLAB environment, the system is best used as a research platform, and not as a product development environment -- end-user software is ideally re-implemented in a compiled language, after a suitable approach has been identified and extensively tested. The process of identifying and testing an approach involves more than just computation, but also data exploration and investigation - an area which is helped by the deep integration with the EEGLAB platform. In the future, this integration will be further strengthened, bringing rich statistical learning and signal processing into routine EEG analysis workflows. The toolbox has been developed by C. Kothe at the Swartz Center, inspired by the preceding PhyPA BCI toolbox created by C. Kothe and T. Zander at the Chair for Human-Machine Systems, Berlin Institute of Technology.
Proper citation: BCILAB (RRID:SCR_007013) Copy
https://github.com/Illumina/strelka/
Software for somatic single nucleotide variant (SNV) and small indel detection from sequencing data of matched tumor-normal samples. Strelka2 germline and somatic small variant caller.
Proper citation: Strelka2 (RRID:SCR_005109) Copy
https://bioconductor.org/packages/FlowSorted.Blood.EPIC/
Software package includes new cell reference for adult peripheral blood deconvolution arrayed using Illumina HumanMethylationEPIC.Optimized library for reference based deconvolution of whole blood biospecimens assayed using Illumina HumanMethylationEPIC BeadArray.
Proper citation: FlowSorted.Blood.EPIC (RRID:SCR_022540) Copy
https://github.com/AlgoLab/CouGaR-g
Source code for "Accurate and Fast Clade Assignment via Deep Learning and Frequency Chaos Game Representation".
Proper citation: CouGaR-g (RRID:SCR_022952) Copy
https://github.com/protofilamentdude/Protofilament-Bending-Models
Code is written to be run with Matlab version r2020b or higher. Model accepts wave assay pulse amplitude data, and simultaneously solves and fits protofilament deflection models to deduce fundamental biophysical properties of microtubule protofilaments.
Proper citation: Protofilament Bending Models (RRID:SCR_023062) Copy
https://github.com/caraweisman/abSENSE
Software to interpret undetected homolog.Method that calculates probability that homolog of given gene would fail to be detected by homology search in given species, even if homolog were present and evolving normally.
Proper citation: abSENSE (RRID:SCR_023223) Copy
https://github.com/DeNardoLab/BehaviorDEPOT
Software tool for automated behavioral detection based on markerless pose tracking. Behavioral analysis tool to first compile and clean point-tracking output from DeepLabCut, and then classify behavioral epochs using custom behavior classifiers. Used to detect frame by frame behavior from video time series and can analyze results of common experimental assays, including fear conditioning, decision-making in T-maze, open field, elevated plus maze, and novel object exploration. Calculates kinematic and postural statistics from keypoint tracking data from pose estimation software outputs.
Proper citation: BehaviorDEPOT (RRID:SCR_023602) Copy
https://github.com/DigitalHealthcareLab/22ActionRecognitionTool
Software tool for multi view child motor development dataset for AI-driven assessment of child development project.
Proper citation: 22ActionRecognitionTool (RRID:SCR_023552) Copy
https://github.com/fhcrc/seqmagick/
Software application to expose file format conversion in BioPython in convenient way. Imagemagick like frontend to Biopython SeqIO.
Proper citation: seqmagick (RRID:SCR_024331) Copy
https://gitlab.com/tjobbertjob/ms-review-paper
Variability analysis of proteomics data used for deep learning.
Proper citation: ms-variability-analysis (RRID:SCR_024531) Copy
https://github.com/PacificBiosciences/unanimity
Software to generate highly accurate single molecule consensus reads.
Proper citation: CCS (RRID:SCR_024379) Copy
https://github.com/cancerit/alleleCount
Software package to prevent code duplication. Support code for NGS copy number algorithms. Generates count of coverage of each allele ACGT at that location given any filter settings.
Proper citation: alleleCount (RRID:SCR_023961) Copy
https://github.com/ejcorn/mouse_abi_tool
Software tool to pull gene expression from Allen Brain Institute API in same annotation space as structural connectome.
Proper citation: Mouse_abi_tool (RRID:SCR_023831) Copy
https://github.com/VioletteChiara/AnimalTA
Software video tracking tool for tracking and analysing animal movement in different environments.
Proper citation: AnimalTA (RRID:SCR_023784) Copy
Software provides command line interface and Python API for working with Biological Observation Matrix files.
Proper citation: python-biom-format (RRID:SCR_024193) Copy
https://github.com/opensafely-core
The code that runs the OpenSAFELY platform used for analysis of electronic health records data.
Proper citation: OpenSAFELY (RRID:SCR_023790) Copy
http://bioinf.cs.ucl.ac.uk/downloads/MetaPSICOV/
Software tool for accurate prediction of contacts and long range hydrogen bonding in proteins.
Proper citation: MetaPSICOV (RRID:SCR_024517) Copy
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