Search Results for "open cell"
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Showing 100 open source projects for "open cell"
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awesome-single-cell
Community-curated list of software packages and data resources
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc. List of software packages (and the people developing these methods) for single-cell data analysis, including RNA-seq, ATAC-seq, etc. Rapid, accurate and memory-frugal preprocessing of single-cell and single-nucleus RNA-seq data. Find bimodal, unimodal, and multimodal features in your data. Ascend is an R package comprised of fast, streamlined analysis functions optimized to... -
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Seurat
R toolkit for single cell genomics
Seurat is a comprehensive R toolkit for single-cell genomics analysis, introduced by the Satija Lab at NYGC. It supports quality control, normalization, clustering, integration of multimodal data (e.g., scRNA‑seq, spatial, CITE‑seq), and visualization. Seurat v5 introduces scalable workflows and spatial transcriptomics support, commonly used in academic and industry research for single-cell studies. -
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Handcalcs
Python library for converting Python calculations into rendered latex
Handcalcs is a Python library that auto-renders calculation code in Jupyter notebooks or LaTeX documents with step-by-step symbolic substitution, giving output a “handwritten” feel. It supports cell magics and auto-LaTeX generation via configurable output options. -
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kallisto
Near-optimal RNA-Seq quantification
kallisto is a program for near-optimal quantification of transcript abundances from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the idea of using pseudoalignment to quickly determine reads and targets’ compatibility, with no need for alignment. According to benchmarks done on a Mac desktop computer, kallisto can quantify 30 million human bulk RNA-seq reads in less than 3 minutes with just the read sequences and a... -
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Smilei
Particle-in-cell code for plasma simulation
Smilei is an open-source electromagnetic Particle-In-Cell code for kinetic plasma simulation. It is designed for high-performance computing and can run on modern supercomputing architectures. The software is co-developed by physicists and computer scientists, which gives it both strong numerical physics capabilities and serious parallel-performance engineering. -
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This application creates off-line atlases of raster maps for various cell phone apps on Android, iPhone and WindowsCE as well as GPS devices (Garmin, Magellan and others)
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NeuroML is an XML-based description language for defining and exchanging neuronal cell, network and modeling data including reconstructions of cell anatomy, membrane physiology, electrophysiological data, network connectivity, and model specification
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atomes
Analysis, visualization, edition of 3D atomistic models
atomes is a Free (Open Source) cross-platform software licensed under the terms of the Affero GPL v3+ license. atomes is a toolbox developed to analyze, to visualize and to create/edit 3D atomic scale models. atomes also provides an advanced input preparation system for further calculations using well known molecular dynamics codes: - Classical MD : DL-POLY and LAMMPS - ab-initio MD : CPMD and CP2K - QM-MM MD : CPMD and CP2K atomes is developed by Dr. Sébastien Le Roux, research... -
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The auditory modeling toolbox (AMT) is a Matlab/Octave toolbox for the development and application of auditory computational models. Over 50 auditory models implemented in Matlab, Octave, C, C++, and Python can be run from Matlab and Octave, on Windows and Linux. The AMT provides a well-structured in-code documentation, includes auditory data required to run the models. It integrates functionality to reproduce the model predictions. Model implementations can be evaluated in two stages,...
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GDSread
GDSread reads and converts Calma GDS stream files .
GDSread is a simple command line utility written in Free Pascal. GDSread can read and convert a Calma GDS stream file and output an ASCII formatted list file and a new GDS file with updated timestamp. If specified - it can modify the output GDS database by scaling it and/or replace cell names. Check out readme.rtf. -
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ePnR
ePnR is an IC block standard cell placement & routing tool
ePnR is a simple Integrated Circuit (IC) block standard cell placement & routing tool. ePnR currently supports only circuit blocks using equal height standard cells arranged in one or more channels of user configurable length. Standard cells are described in a simple text based library (compliant with eLogSim). Placement follows initially the cell call order in the SPICE like circuit input netlist. However, a placement optimization, aiming at minimum weighted accumulated wire length, by... -
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GroIMP
Growth-grammar related Interactive Modelling Platform
Important: Groimp migrates to Gitlab. You can find the latest code at "https://gitlab.com/grogra/groimp/". The version on Sourceforge will not be updated anymore. The modelling platform GroIMP is designed as an integrated platform which incorporates modelling, visualisation and interaction. It exhibits several features which makes itself suitable for the field of biological or ALife modelling: The “modelling backbone” consists in the language XL. It is fully integrated, e.g., the... -
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Allelome.PRO
A pipeline to define allele-specific genomic features
Detecting allelic biases from high-throughput sequencing data requires an approach that maximises sensitivity while minimizing false positives. Here we present Allelome.PRO, an automated userfriendly bioinformatics pipeline, which uses high-throughput sequencing data from reciprocal crosses of two genetically distinct mouse strains to detect allele-specific expression and chromatin modifications. Allelome.PRO extends approaches used in previous studies that exclusively... -
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The Development System for Auditory Modelling (DSAM) is a computational library designed specifically for producing simulations of the auditory system. It brings together many established auditory models within a flexible programming platform.
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MoPAC
The Modular Pipeline for the Analysis of CRISPR screens
To facilitate the comparison of gene essentialities in two or more cell samples, we propose MoPAC (Modular Pipeline for Analysis of CRISPR screens), a Shiny-driven interactive tool for differential essentiality analysis in CRISPR/Cas9 screens. For installation and usage instructions please refer to the wiki page. -
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PMCGPU
Parallel simulators for Membrane Computing on the GPU
Membrane Computing is a new research area (within Natural Computing) that aims to provide computing devices abstracted from the functioning and structure of living cells. These devices are called P systems. The objective of this project (PMCGPU) is to bring together all the researchers working on the development of parallel simulators for P systems, specially those using the GPU (e.g. CUDA, OpenCL, etc). Other parallel platforms are also welcome (multicore and manycore, FPGAs,... -
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The openFuelCell project is a forum to develop open source computational fluid dynamics (CFD) software to model fuel cells. Fuel cells http://en.wikipedia.org/wiki/Fuel_cell are devices that convert hydrogen and oxygen to water and electricity, and are promising renewable energy conversion devices. Computational fluid dynamics tools are used to size and rate fuel cell systems. OpenFoam is an open source CFD toolbox, available for downloading at http://www.openfoam.com/, written in C++ and conforming to the object-oriented paradigm.
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SPARTA
Direct Simulation Monte Carlo (DSMC) Simulator
SPARTA is a parallel DSMC code for performing simulations of low-density gases in 2d or 3d. Particles advect through a hierarchical Cartesian grid that overlays the simulation box. The grid is used to group particles by grid cell for purposes of performing collisions and chemistry. Physical objects with triangulated surfaces can be embedded in the grid, creating cut and split grid cells. -
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chemfiles
Modern library for chemistry file reading and writing
Chemfiles is a modern and high-quality library for reading and writing trajectory files created by computational chemistry simulations program. These trajectories contains atomic positions, velocities, names, topology and sometimes more. Running simulations produce enormous amounts of data, which has to be post-processed to extract physical information about the simulated system. Chemfiles provides an interface to access this information which is - unified: the same code will work with... -
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TX-TL modeling toolbox
Modeling and analysis tools for the TX-TL cell-free expression system
This project contains tools for using the TX-TL cell-free expression system. These tools include component models for simulating and analyzing biomolecular circuits, as well tools for composing circuits and creating more complex systems. NOTE: This project has been shifted to GitHub: https://github.com/BuildACell/txtlsim -
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Virtual Cell
Former home of the Virtual Cell platform (VCell), see http://vcell.org
This project and all source code has moved to GitHub, see https://github.com/virtualcell -
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experix laboratory control system
instrument control, data acquisition display and analysis
Experix is a command-line driven environment for laboratory data acquisition and device control and graphical presentation and analysis of data. Written in C for GNU-Linux . Tested on PC and Raspberry Pi. The core is written very generally in order to support applications by means of script files. Device interfaces: PCMCIA daq (2 devices tested) via kernel module with interrupt handler and memory-mapped data; USB daq (1 device tested) using libusbx; running an equipment servicing program... -
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fNBookForm2 for Mathematica
print sci num with powers (txtbook) + read back
fNBookForm2 prints a number in Textbook Form with powers abbreviations in place of exponents (default). Output is a compressed dressed form textbooks use for significant figures tables. Easy, quality, comprehensive. booknum reads such. an important aspect is that the result maintains both accuracy and precision and has rounding control. doing this sometimees requires careful planning (error-prone complicated conversions). can read them back from textbook (into Mathematica)... -
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...Citation: Yadav B, Peddinti G, Pemovska T, Khan SA, Szwajda A, Tang J, Wennerberg K and Aittokallio T. From drug response profiling to target addiction scoring in cancer cell models. (Submitted)