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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://CRAN.R-project.org/package=ggsurvfit
Software R package for flexible time-to-event figures creation. Used to create figures ready for publication.
Proper citation: ggsurvfit (RRID:SCR_025045) Copy
https://numba.readthedocs.io/en/stable/index.html
Open source JIT compiler that translates subset of Python and NumPy code into fast machine code. Can compile large subset of numerically-focused Python, including many NumPy functions. Has support for automatic parallelization of loops, generation of GPU-accelerated code, and creation of ufuncs and C callbacks.
Proper citation: Numba (RRID:SCR_025056) Copy
https://www.3ds.com/products/simulia/abaqus
Software suite for finite element analysis and computer aided engineering.
Proper citation: Abaqus FEA (RRID:SCR_024997) Copy
https://github.com/aprismatic/prismadb
Software application as cryptographic security layer for relational database systems, that currently supports Microsoft SQL Server, MySQL, MariaDB, PostgreSQL and CockroachDB. Security layer for relational database systems.
Proper citation: Prisma/DB (RRID:SCR_025246) Copy
https://CRAN.R-project.org/package=gridExtra
Softwate R package to work with "grid" graphics, notably to arrange multiple grid-based plots on page, and draw tables. Miscellaneous functions for Grid graphics.
Proper citation: gridExtra (RRID:SCR_025249) Copy
https://github.com/yichun10/bioKGQA-KGT.git
Software contains all scripts and instructions for running Knowledge Graph-based Thought model, which is knowledge graph enhanced LLMs framework for pan-cancer question answering.
Proper citation: bioKGQA-KGT (RRID:SCR_025176) Copy
https://github.com/kryptnostic/krypto
Software C++ implementation of multivariate quadratic FHE.
Proper citation: krypto (RRID:SCR_025179) Copy
https://gitlab.com/sysbiobig/movarsim
Software simulator that leverages data-driven information to set both variants and reads characteristics, producing realistic tumoral samples. Computational modelling of cancer-specific variants and sequencing reads characteristics for realistic tumoral sample simulation.
Proper citation: MOVARSim (RRID:SCR_025388) Copy
https://lambada.icm-institute.org
Reference atlas of the developing post-natal mouse brain. Provides data and annotations on distribution of cells and gene expression in mouse brain.
Proper citation: LAMBADA (RRID:SCR_025382) Copy
https://github.com/PhysiCell-Tools/PhysiCell-Studio
Software graphical tool to allow easy editing of (XML) model, create initial positions of cells, run simulation, and visualize results. To contribute, fork and make PRs to the development branch. Used to create, execute, and visualize multicellular model using PhysiCell.
Proper citation: PhysiCell Studio (RRID:SCR_025311) Copy
https://github.com/ingmarboeschen/JATSdecoder
Software metadata and text extraction and text manipulation tool set for statistical programming language R. Facilitates text mining projects on scientific articles in 'NISO-JATS' format by enabling individual selection of metadata and text parts.
Proper citation: JATSdecoder (RRID:SCR_025279) Copy
https://github.com/MannLabs/pydiaid
Software Python package for DIA with automated isolation design. Used for Data-Independent Acquisition providing Automated Isolation Design. Optimally generates dia-PASEF and synchro-PASEF methods and places them optimally within the m/z – ion mobility (IM) plane.
Proper citation: py_diAID (RRID:SCR_025304) Copy
https://shop.sartorius.com/ca/p/incucyte-ai-cell-health-analysis-software-module/BA-04871#
Software for analysis to determine live versus dead cells – no fluorescent dyes needed.
Proper citation: Incucyte Cell-By-Cell Analysis Software Module (RRID:SCR_025367) Copy
https://dokumate.com/knowledgebase/docid/
DokuMate helps standardize and reuse documents, simplifies and speeds-up editing, and automates many tedious tasks. A docId” is one of the “magic” Content Control tag names. A docId is an alphanumerical ID (e.g., “R01-01-C00”, “R01-11-100”, “R01-11-410”, “R01-30-100”) that uniquely identifies and sorts documents (e.g., Schedule C, Exhibit 1, Attachment 4.1, Appendix 1) within a larger set of documents, e.g., all documents belonging to (a) a specific RFP or (b) the set of contracts between a first party and a second party.
Proper citation: DokuMate (RRID:SCR_025402) Copy
https://github.com/TheLeeLab/cameraCalibrationCMOS
Software for performing pixelwise calibration of sCMOS cameras. MATLAB code and instructions for routine camera calibration.
Proper citation: cameraCalibrationCMOS (RRID:SCR_025339) Copy
https://github.com/marbl/Winnowmap
Software tool as long-read mapping algorithm optimized for mapping ONT and PacBio reads to repetitive reference sequences. Winnowmap2 computes each read mapping through collection of confident subalignments. This approach is more tolerant of structural variation and more sensitive to paralog-specific variants within repeats.
Proper citation: Winnowmap (RRID:SCR_025349) Copy
Software tool that helps users write experimental protocols.
Proper citation: Ready Set Potato (RRID:SCR_025289) Copy
https://search.kg.ebrains.eu/?category=Project#904b7981-0c68-4af6-b3bb-3d9a648b3a7c
Continuous 3D reference atlas for postnatal mouse brain.
Proper citation: Developmental Mouse Brain atlas (RRID:SCR_025324) Copy
https://www.yworks.com/products/yed
Software desktop application as general purpose diagramming program with multi-document interface. Cross-platform Java application to generate high-quality diagrams. Runs on Windows, Linux, Mac OS, and other platforms that support Java Virtual Machine.
Proper citation: yEd (RRID:SCR_025325) Copy
Operating software for Thermo Scientific NanoDrop 1000 Spectrophotometer. Free NanoDrop operating software to update your instrument.
Proper citation: Thermo Scientific NanoDrop 1000 Software (RRID:SCR_025282) Copy
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