Tools   Select Another Resource Report Type

https://github.com/ICB-DCM/PESTO

Software customizable toolbox for parameter estimation in MathWorks MATLAB. Offers scalable algorithms for optimization, uncertainty and identifiability analysis which do not depend on any problem-specific assumptions.

Proper citation: PESTO (RRID:SCR_016891) Copy   

•   Source: SciCrunch Registry
  

http://cqb.pku.edu.cn/ZhuLab/PPR_Meta

Software tool to identify metagenomic sequences of phages, chromosomes or plasmids. Used for identifying phages and plasmids from metagenomic fragments using deep learning., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PPR-Meta (RRID:SCR_016915) Copy   

•   Source: SciCrunch Registry
  

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM

Software tool for inference using permutation methods. Requires Matlab or Octave. Can be executed from inside either environment, or directly from the shell and can be called from scripts. For users who are familiar with statistics and willing to use experimental analysis tools.

Proper citation: PALM (RRID:SCR_017029) Copy   

•   Source: SciCrunch Registry
  

https://git.io/vymwn

A Matlab adapter class and user interface to control the Reglo ICC peristaltic pump provided by Ismatec.

Proper citation: Reglo ICC control with Matlab (RRID:SCR_016353) Copy   

•   Source: SciCrunch Registry
  

https://sourceforge.net/projects/bva-io/

Software package for interfacing the Brain Vision Analyser data files (load/save) for ongoing development of Matlab routines . This package is also compatible with the EEGLAB software, and may be uncompressed in the plugin folder of this software.

Proper citation: BVA import/export EEGLAB plugin (RRID:SCR_016333) Copy   

•   Source: SciCrunch Registry
  

http://zebeyetrack.org/

Open source software for zebrafish eye tracking and visual stimulation. Used to evoke and track zebrafish eye movement in multiple larvae.Modular software able to control multiple aspects of oculomotor experiment, from stimulus presentation and data acquisition to eye tracking and data analysis, or to simply track eyes in existing video of larval zebrafish. In both cases, eyes of up to six fish can be tracked in parallel.Users can choose to control several alternative setups and optional hardware.

Proper citation: ZebEyeTrack (RRID:SCR_021057) Copy   

•   Source: SciCrunch Registry
  

https://potterswheel.de/

Software MATLAB toolbox for mathematical modeling of time dependent dynamical systems that can be expressed as chemical reaction networks or ordinary differential equations. Allows to automatically calibrate model parameters by fitting model to experimental measurements.Fits model to several data sets at once (multi-experiment fitting). Accessible via graphical user interfaces, from command line and scripts,determines parameter identifiability and confidence intervals,imports and exports SBML models and supports biochemical network modeling.

Proper citation: PottersWheel (RRID:SCR_021118) Copy   

•   Source: SciCrunch Registry
  

https://gramian.de

Software for empirical gramians for model reduction of (nonlinear) input-output systems.

Proper citation: Empirical Gramian Framework (RRID:SCR_015043) Copy   

•   Source: SciCrunch Registry
  

http://mariannebezaire.com/simtracker/

MATLAB-based tool for use with NEURON network models. It supports the modeler with model design, organization, execution (including on supercomputers), analysis, and reproducibility.

Proper citation: SimTracker (RRID:SCR_014735) Copy   

•   Source: SciCrunch Registry
  

https://uk.mathworks.com/help/deeplearning/ug/deep-learning-in-matlab.html

Software application provides simple MATLAB commands for creating and interconnecting layers of deep neural network.

Proper citation: Deep Learning Toolbox (RRID:SCR_024747) Copy   

•   Source: SciCrunch Registry
  

https://github.com/csitron/Microscopy_tif_Channel_Quant_MATLAB

Software application for quantification of fluorescence channel area in TIFF images using MATLAB.

Proper citation: Microscopy_tif_Channel_Quant_MATLAB (RRID:SCR_026999) Copy   

•   Source: SciCrunch Registry
  

https://www.car-net.org/tools

Software function as Matlab implementation of the TFA as specified in the White Paper (2015). An example of use on the supplied data (tfa_sample_data.txt) is given in tfa_demo.m and results are reported at the end of this report.

Proper citation: CARNet TFA Function (RRID:SCR_027022) Copy   

•   Source: SciCrunch Registry
  

http://ompc.juricap.com

OMPC aims to enable reuse of the huge open and free code base of MATLAB on a free and faster growing Python platform. Running Python and MATLAB in a single interpreter avoids issues with running two separate applications. Python adds general purpose programming libraries to the convenient syntax of the language of technical computing. OMPC is not an interpreter, it lets Python to do the work. This means that if Python gets faster OMPC gets faster too. OMPC translates the m-files preserving the structure of the original programs as much as possible. Although OMPC comes with a library that emulates the features of numerical array of MATLAB there is nothing that will stop you from running the translated code the way you like it. This means that you could run the OMPC generated code on IronPython, Jython, PyPy or whatever else if you write your own numerical class. Sponsors: This resource is supported by RIKEN Brain Science Institute.

Proper citation: An Open-Source MATLAB-to-Python Compiler (RRID:SCR_008409) Copy   

•   Source: SciCrunch Registry
  

http://www.nitrc.org/projects/mixge/

MATLAB Toolbox which provides a mixed effect model for gene-environment interaction (MixGE) on neuroimaging phenotypes, such as structural volumes and tensor-based morphometry (TBM). This model incorporates both fixed and random effects of genetic-set and environment interaction in order to investigate homogeneous and heterogeneous contributions of sets of genetic variants and their interactions with environmental risks to phenotypes.

Proper citation: Mixed Effect Model of Genetic-Set and Environment Interaction (RRID:SCR_015514) Copy   

•   Source: SciCrunch Registry
  

https://trendscenter.org/software/

Software toolbox which finds and displays temporal relations amongst components. This can help determine causal relations in the brain.

Proper citation: Functional Network Connectivity (FNC) (RRID:SCR_015731) Copy   

•   Source: SciCrunch Registry
  

https://nxr.northwestern.edu/digital-rat

Software for a 2D elastic beam model that can be used to model quasistatic bending of the vibrissa to compute forces and bending moments at the base. Elastica2D is part of the Digital Rat software project that that aims to enable morphologically and mechanically accurate modelling of the rat head and vibrissal (whisker) array.

Proper citation: Elastica2D (RRID:SCR_015858) Copy   

•   Source: SciCrunch Registry
  

https://omictools.com/rnacompete-tool

Method for the systematic analysis of RNA binding specificities that uses a single binding reaction to determine the relative preferences of RBPs for short RNAs that contain a complete range of k-mers in structured and unstructured RNA contexts. RNAcompete identifies expected and previously unknown RNA binding preferences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: RNAcompete (RRID:SCR_015900) Copy   

•   Source: SciCrunch Registry
  

https://sourceforge.net/projects/gftbox/

Analysis software for analysis of finite elements and simulations of 3D shape changes in a tissue that result from patterns of growth. It works with Matlab to model biological growth of leaves, petals, and similar organs.

Proper citation: GrowthToolbox (RRID:SCR_015754) Copy   

•   Source: SciCrunch Registry
  

http://microbetracker.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone. Software for bacterial microscopy image analysis. It is designed to detect and outline bacterial cells in microscopy images and to analyze fluorescence signal inside them.

Proper citation: MicrobeTracker (RRID:SCR_015939) Copy   

•   Source: SciCrunch Registry
  

https://github.com/brain-life/encode

Software that implements a framework to encode structural brain connectomes into multidimensional arrays (tensors). Encoding Connectomes provides an agile framework for computing over connectome edges and nodes.

Proper citation: Linear Fascicle Evaluation (RRID:SCR_016153) Copy   

•   Source: SciCrunch Registry