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http://www.prisma-statement.org/

Evidence based minimum set of items for reporting in systematic reviews and meta analyses. Focuses on reporting of reviews evaluating randomized trials, but can also be used as basis for reporting systematic reviews of other types of research, particularly evaluations of interventions.

Proper citation: PRISMA (RRID:SCR_018721) Copy   

•   Source: SciCrunch Registry

https://github.com/mrc-ide/PhyDyn

Sofware package for performing Bayesian phylogenetic inference under models that deal with structured populations with complex population dynamics. Enables simultaneous estimation of epidemiological parameters and pathogen phylogenies. Epidemiological modelling in BEAST.

Proper citation: PhyDyn (RRID:SCR_018544) Copy   

•   Source: SciCrunch Registry

https://github.com/stekhoven/missForest

Software R package to impute missing values particularly in case of mixed type data. Non parametric, mixed type imputation method for any type of data for statistical software R. Predicts missing values.

Proper citation: missForest (RRID:SCR_018543) Copy   

•   Source: SciCrunch Registry

https://pyrx.sourceforge.io/

Open source virtual screening software for computational drug discovery with intuitive user interface. Runs on operating systems Linux, Windows, and Mac OS. Used to screen libraries of compounds against potential drug targets.

Proper citation: PyRx (RRID:SCR_018548) Copy   

•   Source: SciCrunch Registry

https://opencor.ws/

Open source cross platform modeling environment for reproducible science. Used to organise, edit, simulate and analyse models described in CellML format, using SED-ML and COMBINE archives.

Proper citation: OpenCOR (RRID:SCR_019001) Copy   

•   Source: SciCrunch Registry

https://www.crd.york.ac.uk/PROSPERO

International database of prospectively registered systematic reviews in health and social care, welfare, public health, education, crime, justice, and international development, where there is health related outcome. Key features from review protocol are recorded and maintained as permanent record. Aims to provide comprehensive listing of systematic reviews registered at inception to help avoid duplication and reduce opportunity for reporting bias by enabling comparison of completed review with what was planned in protocol.

Proper citation: PROSPERO (RRID:SCR_019061) Copy   

•   Source: SciCrunch Registry

http://www.softberry.com/berry.phtml?topic=fgenesh_plus_plus&group=help&subgroup=pipelines

Software tool as pipeline for automatic prediction of genes in eukaryotic genomes based on Softberry gene finding software.

Proper citation: Fgenesh plus plus (RRID:SCR_018928) Copy   

•   Source: SciCrunch Registry

https://docs.osparc.io

Simulation platform that enables users to create, access, tune, and run models or computational algorithms through web based interface. Web interactive simulation platform that hosts SPARC computational models and solvers. Allows collaborative development and sharing, model coupling and cloud based execution, data visualization and analysis, and ensures sustainability of computational models developed within SPARC. Enables users to create predictive, multiscale, multi-physics models spanning from modulation sources acting on peripheral nervous system (PNS) to resulting modulation of organ functional response.

Proper citation: o²S²PARC (RRID:SCR_018997) Copy   

•   Source: SciCrunch Registry

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://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