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Showing 29 open source projects for "cell"
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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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KherveSheet
Excel for scientists: high-quality plots, Python in cells, AI side bar
...You have full control over axes, scales, ticks, titles and grids. Curve fitting and peak fitting are supported, with goodness-of-fit reporting overlaid on the plot. Every cell can also run a full Python program, not just a formula. An integrated AI assistant can generate the cell code from a plain-language description if needed. Learn by doing with 300 ready-made scientific examples covering plotting, data analysis, fitting and simulation. Built entirely in Python, KherveSheet adds a familiar Excel-style grid, an optimisation solver, and a native .ksheet format with CSV and Excel import/export. ... -
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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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XRD CUBIC
Simulate crystal cell length (a), Miller indices {h, k, l}, d-spacing
This is a basic computer program (coded in Python) to simulate possible unit crystal cell length (a), Miller indices - {h, k, l} and interplanar spacing (d) for cubic crystals from observed (experimental) X-ray diffraction (XRD) angle, 2-theta. It can simulate all these possible crystal lattice parameters for cubic crystal systems between the given 2–theta values within the range of specified cell length (a) limits. 1. -
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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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SCiDA Pro
Program for solar cell production data analysis
The purpose of the SCiDA Pro program is to help with processing solar cell production data. It has the following features: - Able to handle large data sets in a fast way (e.g. plotting 100k cell data takes a few seconds) - Easy data filtering - Easy generation of a data summary report - Extensive data plotting features - Cross-platform (Windows/Linux/MacOS) - Supports multiple languages -
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DESC Pro
Discrete event simulation for solar cell production
The aim of the DESC Pro program is to try to capture the dynamics of modern solar cell production lines using discrete event simulation techniques. All process and transportation events within the whole line can in principle be included in the simulations, which gives the advantage that dynamic aspects such as planned maintenance and random micro-stops can easily be taken into account. -
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DEBay
Deconvolutes qPCR data to estimate cell-type-specific gene expression
DEBay: Deconvolution of Ensemble through Bayes-approach DEBay estimates cell type-specific gene expression by deconvolution of quantitative PCR data of a mixed population. It will be useful in experiments where the segregation of different cell types in a sample is arduous, but the proportion of different cell types in the sample can be measured. DEBay uses the population distribution data and the qPCR data to calculate the relative expression of the target gene in different cell types in the sample. ... -
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Molecular Dynamics Studio
Molecular Dynamics Cell Construction
...NanoEngineer-1 is a molecular CAD software written by Nanorex and provides the user an easy way to create molecules, while the software modifications allow the user to type atoms using multiple force fields. PACKMOL can generate a random collection of molecules using the molecule templates from NanoEngineer-1 thus providing the initial MD cell. Modifications to PACKMOL allow the atom type data to be passed through to the MSI2LMP software. MSI2LMP creates a LAMMPS input file based on class I or class II force fields. MSI2LMP was modified to use numerically coded force field data generated by NanoEngineer-1. The MMP file format was extended and integrated into all three software applications. ... -
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pyfolio
Portfolio and risk analytics in Python
pyfolio is a Python library for performance and risk analysis of financial portfolios developed by Quantopian Inc. It works well with the Zipline open source backtesting library. At the core of pyfolio is a so-called tear sheet that consists of various individual plots that provide a comprehensive image of the performance of a trading algorithm. Here's an example of a simple tear sheet analyzing a strategy. Quantopian also offers a fully managed service for professionals that includes... -
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Microarray Integrator (MAI)
Microarray Integrator for heterogeneous human/mouse Affymetrix arrays
The Microarray Integrator is freely available programs to integrate heterogeneous Affymetrix microarrays for human and mouse. The cell-type-specific genes or condition-specific genes can be screened in the integrated microarrays by MAI result. -
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FAST Simulations
An Open source Analysis and SImulation Toolbox for Fuel Cells
FAST is an Analysis and Simulation Toolbox (FAST) for Fuel Cells (FC) FAST-FC is the doctorate work of David B. Harvey and was developed with support from the U.S. DOE, Ballard, and Queen's University. Derivative works of FAST-FC include FC-APOLLO which is a forked branch of this project intended to capture the code state at the exit of the funded DOE project. FAST-FC is the open and active community branch. FAST-FC is developed and maintained by the original creator and... -
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Virus QSP Modeling
C++ and Python code for simulating RNA virus replication
Stochastic simulation model of poliovirus Sabin-to-Mahoney genetic state transition (C++ code). Models genotypes, virus populations, and quasispecies cloud. Simulates replication error and copy-choice recombination. Various parameters guiding the model are user-specified. Python code post-processes simulation output to produce report files. -
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HuaweiConfigurationManager
Improve the efficiency of R&D engineers
This is old project please refer to https://sourceforge.net/projects/emaossmanager/ Improve the efficiency of R&D engineers Parsers BSC&RNC MML Scripts BSC&RNC Alarms logs BSC&RNC Operation logs ENODEB XML Configuration ENODEB SON Log BSC&RNC&NODEB&ENODEB License NODEB&ENODEB Inventory M2000 Alarm logs M2000 OpLog logs M2000 CME NBI R915 M2000 EAM configuration ASSET Cell export file Tools & Analyzers Command View Device GUI BSC&RNC View Compare Manager SQL Connection View Template Handle Switch View MML Redirection Reader Fault Diagnosis SON Dashboard Operation log Analysis NodeB XML2MML MML Discrepancy Geo-data Manager KMZ Generator SQL Expert MapInfo Export Backup Manager Export Manager Aircom Asset Northbound Interface -
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FABS
Fluorescence and absorption spectroscopy made easy
FABS is a program designed to run a fluorescence/absorption spectrometer on Windows. The program analyzes spectra and provides graphs and data files. Users may choose to input video files from cell phones or other cameras, still images, or even live streams of video from webcams. FABS can perform any necessary calibration and image preprocessing. Experienced users have a number of more advanced options such as background subtraction, adjustments for nonlinearities in detector response, and graph smoothing. FABS was designed with students in mind, as a way to help high schoolers and undergraduates learn about spectroscopy without paying for expensive equipment and software. ... -
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Spatio-temporal simulation environment (STSE) is set of tools used to perform spatio-temporal simulations, dedicated mainly to biological systems. Main development language is Python. Tools are currently based on: EPD, VTK, qhull, openalea, PlantGL.
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calc2booktab.latex
Script for OpenOffice/LibreOffice to convert tables to Latex-Code
UPDATE: The project was moved to github (https://github.com/schober-ch/calc2booktab). The soruceforge page won't get any bugfixes, please use the github repo if you want to try this macro. -------------------------------------------------------------------------- A Python extension for OpenOffice/LibreOffice to convert selected cells to LaTeX-Code. Its similar to Calc2Latex, but typographic formatting is more advanced (numeric columns, dcolumn-package, booktab-package) Script is... -
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PolyCTLDesigner
Python scripts for designing polyepitope T-cell immunogens
...PolyCTLDesigner is also able to choose antigenic peptides covering selected HLA repertoire with desired redundancy rate. Given the antigen sequences PolyCTLDesigner is also able to select T-helper epitopes. For predicting T-cell epitopes it uses TEpredict. -
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Application to create 'electronic fluorescent pictographic' representations of gene expression patterns. Created at the Provart lab of the department of Cell & Systems Biology, University of Toronto.
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Ablator
A tool for automating laser ablations for neuroscience
Ablator is a suite of software that automates the microscopic detection of cell targets and also directs a 2-photon microscope to lesion these targets in arbitrary patterns for neuroscience research. See Hayes et al 2012 for an example of its usage (http://www.pnas.org/content/109/21/8286.abstract). -
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colonyzer image analysis software
Image analysis estimating cell density in arrayed microbial cultures
Image analysis software for quantification of cell density in microbial cultures (e.g. S. cerevisiae) growing on solid agar plates. Specialises in detection of extremely low cell densities. Forms part of the Quantitative Fitness Analysis (QFA) workflow: http://research.ncl.ac.uk/qfa/ Suitable for high-throughput, genome-wide analysis of culture libraries when combined with the following qfa R package: http://qfa.r-forge.r-project.org/ This is the version presented, used and demonstrated in the following manuscripts: Lawless et al. 2010 http://dx.doi.org/10.1186/1471-2105-11-287 Addinall et al. 2011 http://dx.doi.org/10.1371/journal.pgen.1001362 Chang et al. 2011 http://dx.doi.org/10.1534/g3.111.000216 Banks et al. 2012 http://dx.doi.org/10.3791/4018 Development has been moved to github, where Colonyzer has undergone several recent improvements, particuarly making installation easier and analysis faster: https://github.com/CnrLwlss/Colonyzer -
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Prediction of MHC class I- and MHC class II-restricted T-cell epitopes. Prediction of proteasomal/immunoproteasomal processing of antigens. Prediction of peptide-TAP binding.
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CancerVaccine
In silico vaccination experiment to determine best vaccination schedul
This project is a simplified representation of the main immune system cells and their interactions. The aim is to simulate the effect of the introduction of a cancer vaccine cell which would stimulate the immune response against the tumor-associated antigen, and consequently against cancer cells themselves. In vivo vaccination experiments take very long to complete, so it would be useful to simulate these experiments such that the best schedule of vaccination is determined that would result in control of the cancer cell population. -
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""" E-Cell's source code repository has moved to GitHub! https://github.com/ecell The development of E-Cell now continues on GitHub. The Subversion repository was abandoned. """ E-Cell System is an object-oriented software suite for modeling, simulation, and analysis of large scale complex systems such as biological cells. It allows many components driven by multiple algorithms with different timescales to coexist in a model.
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FociCounter is a simple and user-friendly program for analysis of gamma-H2AX foci. It allows to determine the number of foci in a single cell, a foci intensity as well as a cell intensity.
