Tools   Select Another Resource Report Type

https://github.com/GATB/MindTheGap

Software tool to perform detection and assembly of DNA insertion variants in NGS read datasets with respect to reference genome.Used to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome.

Proper citation: MindTheGap (RRID:SCR_024115) Copy   

•   Source: SciCrunch Registry

https://jydu.github.io/maffilter/

Software tool for analysis of genome alignments. It parses and manipulates MAF files as well as more simple fasta files. Despite various filtering options and format conversion tools, MafFilter can compute a wide range of statistics including phylogenetic trees, nucleotide diversity, inferrence of selection, etc.

Proper citation: MafFilter (RRID:SCR_024105) Copy   

•   Source: SciCrunch Registry

https://sparta.readthedocs.io/en/latest/

Software workflow aimed at analyzing single-end Illumina RNA-seq data. The software is supported on Windows, Mac OS X, and Linux platforms.

Proper citation: sparta (RRID:SCR_024349) Copy   

•   Source: SciCrunch Registry

http://maude.cs.illinois.edu/w/index.php/The_Maude_System

Software high performance reflective language and system supporting both equational and rewriting logic specification and programming for wide range of applications.Supports equational specification and programming, rewriting logic computation.

Proper citation: Maude (RRID:SCR_024108) Copy   

•   Source: SciCrunch Registry

https://github.com/Pas-Kapli/mptp

Software tool for single locus species delimitation. Implements fast method to compute the ML delimitation from inferred phylogenetic tree of the samples.Used to handle very large biodiversity datasets.

Proper citation: mPTP (RRID:SCR_024121) Copy   

•   Source: SciCrunch Registry

https://github.com/bartongroup/yanosim

Software tool as read simulator for nanopore DRS datasets.

Proper citation: Yanosim (RRID:SCR_024363) Copy   

•   Source: SciCrunch Registry

http://ugovaretto.github.io/molekel/

Open source multi platform molecular visualization program.

Proper citation: Molekel (RRID:SCR_024122) Copy   

•   Source: SciCrunch Registry

https://www.mrtrix.org/

Software tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses.

Proper citation: MRtrix3 (RRID:SCR_024123) Copy   

•   Source: SciCrunch Registry

https://mia.sourceforge.net/

Software toolkit for gray scale medical image analysis. Provides combination of command line tools, plug-ins, and libraries that make it possible to run image processing tasks interactively in command shell and prototype algorithms as shell scripts. MIA is build around a plug-in structure that makes it easy to add functionality without compromising the original code base, and it makes use of wide variety of external libraries that provide additional functionality.

Proper citation: MIA (RRID:SCR_024081) Copy   

•   Source: SciCrunch Registry

https://www.eneuro.org/content/10/5/ENEURO.0127-22.2023

Open source, adaptable tracking system for multiple rodents. Scalable and customizable system for tracking and behavior assessment consists of Raspberry Pi based video and RFID acquisition. Maximum of six rodents of any coat color can be tracked simultaneously in any user defined arena with few restrictions. For pose estimation and travel trajectory analysis, PyMouseTracks supports interfacing with open source packages such as DeepLabCut and Traja.

Proper citation: PyMouseTracks (RRID:SCR_024453) Copy   

•   Source: SciCrunch Registry

http://datamares.org

Open source, and interactive platform to resolve trans disciplinary problems related to coastal and marine ecosystem. Data sharing and science communication portal holds amounts of fishery, reef, and mangrove data pertaining to Gulf of California and Mexico specific oceans, and delivers this information in interactive and easily digestible manner. Consistently expands library of datasets while improving functionality and overall usability of the platform. Facilitate access to scientific knowledge and data to promote transparency, education, and deeper understanding of Mexico’s ecosystems and their biodiversity to bridge gap between science and design process of conservation and resource management programs.

Proper citation: DataMares (RRID:SCR_024575) Copy   

•   Source: SciCrunch Registry

https://codemeta.github.io/codemeta-generator/

Web application that creates CodeMeta files.

Proper citation: CodeMeta Generator (RRID:SCR_024601) Copy   

•   Source: SciCrunch Registry

https://www.softwareheritage.org/

Software Heritage provides service for archiving and referencing historical and contemporary software with focus on human readable source code. The site was unveiled in 2016 by Inria and is supported by UNESCO. The project itself is structured as non‑profit multi‑stakeholder initiative.

Proper citation: Software Heritage (RRID:SCR_024602) Copy   

•   Source: SciCrunch Registry

https://proplot.readthedocs.io/en/stable/

Software tool as succinct matplotlib wrapper for making publication quality graphics.

Proper citation: ProPlot (RRID:SCR_024584) Copy   

•   Source: SciCrunch Registry

https://www.photometrics.com/products/ocular

Photometrics acquisition software to capture, save and publish images and movies. Allows users of color and monochrome cameras to capture high quality images and videos from their microscope or lens system.

Proper citation: Ocular (RRID:SCR_024467) Copy   

•   Source: SciCrunch Registry

https://ebrc.org/

Non-profit, public-private partnership dedicated to bringing together inclusive community committed to advancing engineering biology to address national and global needs. We showcase cutting-edge research in engineering biology, identify pressing challenges and opportunities in research and application, articulate compelling research roadmaps and programs to address them, and provide timely access to other key developments in engineering biology.

Proper citation: Engineering Biology Research Consortium (RRID:SCR_024578) Copy   

•   Source: SciCrunch Registry

https://www.eneuro.org/content/10/8/ENEURO.0212-23.2023

Simple, lightweight, and low cost customizable multielectrode array for Local Field Potential recordings. Used to collect LFP data from different brain regions simultaneously in rats. Can be modified to record single unit and multiunit activity in addition to LFP activity using both wired and wireless neural data acquisition systems.

Proper citation: Customizable Multielectrode Array (RRID:SCR_024551) Copy   

•   Source: SciCrunch Registry

https://seismo.berkeley.edu/

Acts as part of statewide earthquake monitoring system, the California Integrated Seismic Network. Conducts essential research on earthquakes and solid earth processes while collecting and delivering high quality geophysical data. Data from these geophysical networks are recorded digitally and are archived at the Northern California Earthquake Data Center, which is located at the Berkeley Seismological Lab.

Proper citation: Berkeley Seismological Laboratory (RRID:SCR_024552) Copy   

•   Source: SciCrunch Registry

https://sparrow-data.org/

Software for managing geochemical data created by individual geochronology laboratory. Designed for flexibility and extensibility, so that it can be tailored to the needs of individual analytical labs that manage wide variety of data. Database set up for metadata tracking.

Proper citation: Sparrow-data (RRID:SCR_024432) Copy   

•   Source: SciCrunch Registry

https://biocodecommons.org/

Platform provides resources for genomic observations from collection to analysis and publication. Works with standards community to ensure clear vocabularies and useful ontologies for biological resources and related assets. Biocode Commons is also collaborating on development of Biological Collections Ontology, working to better integrate ontologies, vocabularies, and relevant standards that are related to BCO.

Proper citation: Biocode Commons (RRID:SCR_024553) Copy   

•   Source: SciCrunch Registry