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https://github.com/jstjohn/SimSeq

An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential for chimeric reads, and non-biotinylated fragment pull down in mate-pair libraries .

Proper citation: SimSeq (RRID:SCR_006947) Copy   

•   Source: SciCrunch Registry

http://www.neuroconstruct.org/

Software for simulating complex networks of biologically realistic neurons, i.e. models incorporating dendritic morphologies and realistic cell membrane conductance, implemented in Java and generates script files for the NEURON and GENESIS simulators, with support for other simulation platforms (including PSICS and PyNN) in development. neuroConstruct is being developed in the Silver Lab in the Department of Neuroscience, Physiology and Pharmacology at UCL and uses the latest NeuroML specifications, including MorphML, ChannelML and NetworkML. Some of the key features of neuroConstruct are: Creation of networks of biologically realistic neurons, positioned in 3D space. Complex connectivity patterns between cell groups can be specified for the networks. Can import morphology files in GENESIS, NEURON, Neurolucida, SWC and MorphML format for inclusion in network models. Simulations can be run on the NEURON or GENESIS platforms. Cellular processes (synapses/channel mechanisms) can be imported from native script files or created in ChannelML. Recording of simulation data generated by the simulation and visualization/analysis of data. Stored simulation runs can be viewed and managed through the Simulation Browser interface.

Proper citation: neuroConstruct (RRID:SCR_007197) Copy   

•   Source: SciCrunch Registry

http://www.ikaros-project.org/

Ikaros is an open infrastructure for system level modeling of the brain including databases of experimental data, computational models and functional brain data. The system makes heavy use of the emerging standards for Internet based information and makes all information accessible through an open web-based interface. In addition, Ikaros can be used as a control architecture for robots which in the extension will lead to the development of a brain inspired robot architecture. The main components of the Ikaros systems are: a platform independent simulation kernel; a set of computational brain models; a set of I/O modules for interfacing with data files and peripheral such as robots or video cameras; tools for building systems of interconnected models; a plug-in architecture that allows new models to be easily added to the system; and a database with data from learning experiments that can be used for validation of the computational models.

Proper citation: Ikaros Project (RRID:SCR_007391) Copy   

•   Source: SciCrunch Registry

http://www.mcell.cnl.salk.edu/

Software modeling tool for realistic simulation of cellular signaling in complex 3-D subcellular microenvironment in and around living cells. Program that uses spatially realistic 3D cellular models and specialized Monte Carlo algorithms to simulate movements and reactions of molecules within and between cells.

Proper citation: MCell (RRID:SCR_007307) Copy   

•   Source: SciCrunch Registry

https://autodocksuite.scripps.edu/adt/

Software graphical user interface to help to set up which bonds will treated as rotatable in the ligand and to analyze dockings. Used for automated docking with selective receptor flexibility. Designed to predict how small molecules, such as substrates or drug candidates, bind to receptor of known 3D structure.

Proper citation: AutoDockTools (RRID:SCR_026401) Copy   

•   Source: SciCrunch Registry

https://igit.informatik.htw-dresden.de/aagef650/spheroidsegdedeb

Software minimal tool for segmentation of irradiated tumor spheroids using optimized U-Net.

Proper citation: SpheroidSegDeDeb (RRID:SCR_026409) Copy   

•   Source: SciCrunch Registry

https://www.brainlab.com/surgery-products/overview-neurosurgery-products/

Privately held German medical technology company headquartered in Munich, Bavaria. Brainlab develops software and hardware for radiotherapy and radiosurgery, and the surgical fields of neurosurgery, ENT and craniomaxillofacial, spine surgery, and traumatic interventions. Brainlab software and hardware devices create and enhance data to improve critical surgeries, radiosurgery treatments and operating room efficiency.

Proper citation: BrainLab (RRID:SCR_026474) Copy   

•   Source: SciCrunch Registry

https://github.com/fzj-inm1-bda/siibra-python/

Software interface for interacting with brain atlases. Python client to brain atlas framework that integrates brain parcellations and reference spaces at different spatial scales, and connects them with broad range of multimodal regional data features. It aims to facilitate programmatic and reproducible incorporation of brain parcellations and brain region features from different sources into neuroscience workflows.

Proper citation: siibra-python (RRID:SCR_026596) Copy   

•   Source: SciCrunch Registry

https://github.com/ddarriba/modeltest

Software tool for selecting the best-fit model of evolution for DNA and protein alignments. Used for selection of DNA and Protein evolutionary models.

Proper citation: modeltest (RRID:SCR_026633) Copy   

•   Source: SciCrunch Registry

https://archive.ics.uci.edu/

Collection of databases, domain theories, and data generators that are used by machine learning community for empirical analysis of machine learning algorithms. Datasets approved to be in the repository will be assigned Digital Object Identifier (DOI) if they do not already possess one. Datasets will be licensed under a Creative Commons Attribution 4.0 International license (CC BY 4.0) which allows for the sharing and adaptation of the datasets for any purpose, provided that the appropriate credit is given

Proper citation: UCI Machine Learning Repository (RRID:SCR_026571) Copy   

•   Source: SciCrunch Registry

https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2

Software tool to call somatic short mutations via local assembly of haplotypes. Somatic variant caller that uses local assembly and realignment to detect SNVs and indels.

Proper citation: Mutect2 (RRID:SCR_026692) Copy   

•   Source: SciCrunch Registry

https://jnm.snmjournals.org/content/46/6/1023.long

Software to evaluate mean absorbed doses to organs and tumors in radionuclide images, providing simple and fast solution for radionuclide imaging and treatment of new drugs in clinical trials. Calculates radiation doses to organs and the whole body based on established human body models.

Proper citation: OLINDA/EXM (RRID:SCR_026835) Copy   

•   Source: SciCrunch Registry

https://gdex.ucar.edu/

Provides data for atmospheric and ocean sciences research. Contains collection of meteorological, atmospheric composition, and oceanographic observations, and operational and reanalysis model outputs, integrated with NSF NCAR High Performance Compute services to support atmospheric and geosciences research. The RDA is managed by the Data Engineering and Curation Services group of the Computational and Information Systems Laboratory at the NSF National Center for Atmospheric Research.

Proper citation: The Geoscience Data Exchange (RRID:SCR_026989) Copy   

•   Source: SciCrunch Registry

https://www.dotmatics.com/capabilities/electronic-lab-notebook

Software for scientific research and development. ELN captures and manages experimental data, while Data Discovery Platform enables users to explore, analyze, and visualize that data to gain insights.

Proper citation: Dotmatics ELN and Data Discovery Platform (RRID:SCR_027029) Copy   

•   Source: SciCrunch Registry

https://www.sbg.bio.ic.ac.uk/docking/ftdock.html

Software tool to discrete two molecules onto orthogonal grids and performs global scan of translational and rotational space.

Proper citation: FTDock (RRID:SCR_027019) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/tguenther/read/src/master/

Software tool to infer family relationships for degraded samples. Used to infer degree of relationship (up to second degree, i.e. nephew/niece-uncle/aunt, grandparent-grandchild or half-siblings) for pair of low-coverage individuals.

Proper citation: READ (RRID:SCR_026958) Copy   

•   Source: SciCrunch Registry

https://github.com/mskilab-org/JaBbA

Software tool to infer junction-balanced genome graphs with high fidelity. Builds genome graph based on junctions and read depth from whole genome sequencing, inferring optimal copy numbers for both vertices (DNA segments) and edges (bonds between segments).

Proper citation: JaBba (RRID:SCR_027134) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/anthakki/prism/src/master/

Software statistical framework that allows simultaneous extraction of tumor sample composition and cell type and sample specific whole-transcriptome profiles from individual bulk RNA-seq samples.

Proper citation: PRISM - Poisson RNA-profile Identification in Scaled Mixtures (RRID:SCR_027136) Copy   

•   Source: SciCrunch Registry

https://github.com/hartwigmedical/hmftools/tree/master/cobalt

Software tool to determine read depth ratios of supplied tumor and reference genomes.

Proper citation: COBALT (RRID:SCR_027132) Copy   

•   Source: SciCrunch Registry

https://www.ethotrack.com/fr/

Video analysis software designed for the study of animal behavior.

Proper citation: Ethotrack (RRID:SCR_027105) Copy   

•   Source: SciCrunch Registry