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http://krasnow1.gmu.edu/CENlab/software.html

Stochastic reaction-diffusion simulator in Java which is used for simulating neuronal signaling pathways.

Proper citation: NeuroRD (RRID:SCR_014769) Copy   

•   Source: SciCrunch Registry

https://www.comsol.com/comsol-multiphysics

General-purpose software platform for modeling and simulating physics-based problems which accounts for coupled or multiphysics phenomena. The platform includes a set of core physics interfaces for common physics application areas such as structural analysis, laminar flow, pressure acoustics, transport of diluted species, electrostatics, electric currents, heat transfer, and Joule heating.

Proper citation: COMSOL Multiphysics (RRID:SCR_014767) Copy   

•   Source: SciCrunch Registry

http://www.lsm.tugraz.at/pcsim/

Software tool for simulating heterogeneous networks composed of different model neurons and synapses. It is intended to simulate networks containing up to millions of neurons and on the order of billions of synapses by distributing the network over different nodes of a computing cluster by using MPI.

Proper citation: PCSIM (RRID:SCR_014770) Copy   

•   Source: SciCrunch Registry

http://mvaspike.gforge.inria.fr/

Tool for modeling and simulating large, complex biological neural networks, particularly pulse-coupled, spiking neural networks. Its main features include modular or hierarchical modeling strategy of networks, phase-coded neurons, event-driven simulation, and integration of standard file formats.

Proper citation: Mvaspike (RRID:SCR_014760) Copy   

•   Source: SciCrunch Registry

http://www.jadesantiago.com/Electrophysiology/IonChannelLab/

Software for kinetic modeling of ion channels which operates on Windows XP or Windows Vista.

Proper citation: IonChannelLab (RRID:SCR_014762) Copy   

•   Source: SciCrunch Registry

http://libroadrunner.org/

Simulation engine for systems and synthetic biology to be used with other software applications. It retains the original functionality of RoadRunner but has changes in performance, back-end design, event handling, new C++ API, and stochastic simulation support.

Proper citation: libRoadRunner (RRID:SCR_014763) Copy   

•   Source: SciCrunch Registry

https://archive.data.jhu.edu/

Open access repository for Johns Hopkins University researchers to share their research data. Data repository is administered by professional curators at JHU Data Services, who will work with depositors to enable future discovery and reuse of your data, and ensure your data is Findable, Accessible, Interoperable and Reusable (FAIR). Each dataset has citation and DOI, facilitating attribution, and connection to research publications.

Proper citation: Johns Hopkins Research Data Repository (RRID:SCR_014728) Copy   

•   Source: SciCrunch Registry

http://rast.nmpdr.org

A SEED-quality automated service that annotates complete or nearly complete bacterial and archaeal genomes across the entire phylogenetic tree. RAST can also be used to analyze draft genomes.

Proper citation: RAST Server (RRID:SCR_014606) Copy   

•   Source: SciCrunch Registry

https://www.deshawresearch.com/resources_desmond.html

Software designed to perform high-speed molecular dynamic simulations of biological systems on conventional commodity clusters, supercomputers and GPUs. This code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on platforms with a large number of processors. It can be used with a single computer.

Proper citation: Desmond (RRID:SCR_014575) Copy   

•   Source: SciCrunch Registry

http://pub.ist.ac.at/ttp/

Software used to simulate tumor progression in various stages of growth in order to study the process' dynamics. The input can be fitness landscape, mutation rate, and cell division time. The output is growth dynamics and other relevant statistics, such as expected tumor detection time and expected appearance time of surviving mutants. The tool is implemented in Java and runs on all operating systems which run a Java Virtual Machine (JVM) of version 1.7 or above.

Proper citation: Tool for Tumor Progression (RRID:SCR_014700) Copy   

•   Source: SciCrunch Registry

https://www.ada.edu.au

A consortium of leading national Australian universities which collects and preserves digital research data and makes these data available for secondary analysis. The consortium provides a data catalogue comprised of seven sub-archives: Social Science, HIstorical, Indigenous, Longitudinal, Qualitative, Crime and Justice, and International. All users can browse and search the catalogue, view study and variable documentation, and download related material. Registered users can also analyze and visualize most data online and users who have completed the relevant undertaking form(s) can download entire studies or subsets of variables. Deposited data are processed, reviewed, and published for research use.

Proper citation: Australian Data Archive (RRID:SCR_014706) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/clustergrammer/

Clustergrammer is a web-based tool for visualizing and analyzing high-dimensional data as interactive and shareable hierarchically clustered heatmaps. Clustergrammer enables intuitive exploration of high-dimensional data and has several optional biology-specific features.

Proper citation: clustergrammer (RRID:SCR_015681) Copy   

•   Source: SciCrunch Registry

https://zenodo.org/record/167621

Simulation environment that combines flexible script language user interface with computational tools in order to setup cardiac electrophysiology in-silico experiments without re-coding at low-level. It aims to include cell excitation, tissue/anatomy models, and stimulation protocols in BeatBox scripts so that simulation run either sequentially or in parallel (MPI) without re-compilation.

Proper citation: BeatBox (RRID:SCR_015780) Copy   

•   Source: SciCrunch Registry

https://github.com/hpardoe/napr/

Cloud-based framework that allows users to estimate the age of individual subjects using cortical thickness maps derived from their own locally processed T1-weighted whole brain MRI scans. The provided age prediction models were trained using (i) relevance vector machines and (ii) Gaussian processes machine learning methods applied to cortical thickness surfaces obtained using Freesurfer v5.3.

Proper citation: NAPR: Neuroanatomical Age Prediction using R (RRID:SCR_015759) Copy   

•   Source: SciCrunch Registry

http://www.braincode.ca

Brain-CODE is a large-scale informatics platform that manages the acquisition and storage of multidimensional data collected from participants with a variety of brain disorders.

Proper citation: Brain-CODE (RRID:SCR_015877) Copy   

•   Source: SciCrunch Registry

https://github.com/cerebis/sim3C/tree/0.1

Software for read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC). Sim3C's potential applications include addressing questions directed at the spatial organization of DNA in samples of eukaryotic tissue, single cells, and microbial communities.

Proper citation: Sim3C (RRID:SCR_015772) Copy   

•   Source: SciCrunch Registry

http://pid.nci.nih.gov

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 27, 2016. Curated database of information about known biomolecular interactions and key cellular processes assembled into signaling pathways. All interactions are assembled into pathways, and can be accessed by performing searches for biomolecules, or processes, or by viewing predefined pathways. This was a collaborative project between the NCI and Nature Publishing Group (NPG) from 2006 until September 22nd, 2012, and is no longer being updated. PID is aimed at the cancer research community and others interested in cellular pathways, such as neuroscientists, developmental biologists, and immunologists. The database focuses on the biomolecular interactions that are known or believed to take place in human cells. It can be browsed as an online encyclopedia, used to run computational analyses, or employed in ways that combine these two approaches. In addition to PID''''s predefined pathways, search results are displayed as dynamically constructed interaction networks. These features of PID render it a useful tool for both biologists and bioinformaticians. PID offers a range of search features to facilitate pathway exploration. Users can browse the predefined set of pathways or create interaction network maps centered on a single molecule or cellular process of interest. In addition, the batch query tool allows users to upload long list(s) of molecules, such as those derived from microarray experiments, and either overlay these molecules onto predefined pathways or visualize the complete molecular connectivity map. Users can also download molecule lists, citation lists and complete database content in extensible markup language (XML) and Biological Pathways Exchange (BioPAX) Level 2 format. The database is supplemented by a concise editorial section that includes specially written synopses of recent important research articles in areas related to cancer research, and specially commissioned Bioinformatics Primers that provide practical advice on how to make the most of other relevant online resources. The database and editorial content are updated monthly, and users can opt to receive a monthly email alert to stay informed about new content. Note: as of September 23, 2012 the PID is no longer being actively curated. NCI will maintain the PID website and data for twelve months beyond September 2012 to allow interested parties to obtain the previously curated data before the site is retired in September 2013.

Proper citation: Pathway Interaction Database (RRID:SCR_006866) Copy   

•   Source: SciCrunch Registry

http://www.nichd.nih.gov/about/org/ncmrr/

Foster development of scientific knowledge needed to enhance the health, productivity, independence, and quality-of-life of people with disabilities. A primary goal of Center-supported research is to bring the health related problems of people with disabilities to the attention of the best scientists in order to capitalize upon the myriad advances occurring in the biological, behavioral, and engineering sciences. The NCMRR uses seven research priorities to help guide its research and research priorities. The research initiatives and opportunities recommended in the Research Plan (PDF - 223 KB) for the National Center for Medical Rehabilitation Research are discussed in terms of seven cross-cutting areas in which increased research effort is needed. Those areas are: * improving functional mobility * promoting behavioral adaptation to functional losses * assessing the efficacy and outcomes to medical rehabilitation therapies and practices * developing improved assistive technologies * understanding whole body system responses to physical impairments and functional changes * developing more precise methods of measuring impairments, disabilities, and societal and functional limitations * training research scientists in the field of rehabilitation In addition, the NCMRR has its own National Advisory Board on Medical Rehabilitation Research that meets twice a year to discuss the Center''s portfolio and research directions. Programs/Program Areas * Behavioral Sciences and Rehabilitation Technologies (BSRT) Program * Biological Sciences and Career Development (BSCD) Program * Pediatric Critical Care and Rehabilitation (PCCR) Program * Spinal Cord and Musculoskeletal Disorders and Assistive Devices (SMAD) Program * Traumatic Brain Injury (TBI) and Stroke Rehabilitation (TSR) Program * Various Supported Networks, Programs, and Initiatives

Proper citation: NCMRR - National Center for Medical Rehabilitation Research (RRID:SCR_006742) Copy   

•   Source: SciCrunch Registry

https://www.tbindsc.org/

The Traumatic Brain Injury Model Systems National Data and Statistical Center (TBINDSC) located at Craig Hospital in Englewood, Colorado, is a central resource for researchers and data collectors within the Traumatic Brain Injury Model Systems (TBIMS) program. The primary purpose of the TBINDSC is to advance medical rehabilitation by increasing the rigor and efficiency of scientific efforts to longitudinally assess the experience of individuals with traumatic brain injury (TBI). The TBINDSC provides technical assistance, training, and methodological consultation to 16 TBIMS centers as they collect and analyze longitudinal data from people with TBI in their communities, and as they conduct research toward evidence-based TBI rehabilitation interventions. The project design includes * The first prospective, longitudinal multi-center study ever conducted which examines the course of recovery and outcomes following the delivery of a coordinated system of acute neurotrauma and inpatient rehabilitation. * Includes large scale follow-up to 20 years post-injury. Available from this site are links to the TBIMS Presentation and TBIMS Update, which has information about the individual model systems and descriptions of the injury and followup data that are being collected. 2007-2012 Project Priorities * Improved long-term outcomes of individuals with TBI by conducting 1-2 site-specific research projects to test innovative approaches that contribute to rehabilitation interventions and evaluating TBI outcomes in accordance with the focus areas identified in NIDRR''s Long-Range Plan. * Improved outcomes for individuals with TBI by participating in at least one collaborative research module project, which may range from pilot research to more extensive studies. * Continued assessment of long-term outcomes of TBI by enrolling at least 35 subjects per year into the longitudinal portion of the TBIMS database. * In carrying out research activities, each Center may select from the following research domains: Health and Function, Employment, Participation and Community Living, and Technology for Access and Function. In addition, each Center must: * Provide a multidisciplinary system of rehabilitation care specifically designed to meet the needs of individuals with TBI. The system must encompass a continuum of care, including emergency medical services, acute care services, acute medical rehabilitation services, and post-acute services; and * Coordinate with the NIDRR funded Model Systems Knowledge Translation Center to provide scientific results and information for dissemination to clinical and consumer audiences.

Proper citation: Traumatic Brain Injury Model Systems National Data and Statistical Center (RRID:SCR_006736) Copy   

•   Source: SciCrunch Registry

http://www.nactem.ac.uk/

The first publicly-funded text mining center in the world that provides text mining services in response to the requirements of the UK academic community. You can find pointers to sources of information about text mining such as links to: * text mining services provided by NaCTeM * software tools, both those developed by the NaCTeM team and by other text mining groups * seminars, general events, conferences and workshops * tutorials and demonstrations * text mining publications NaCTeM is operated by the University of Manchester with close collaboration with the University of Tokyo.

Proper citation: National Centre for Text Mining (RRID:SCR_006738) Copy   

•   Source: SciCrunch Registry