Open Source Python Mathematics Software

Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. For instructions and documentations, please refer to the wiki page. MAGeCK is developed by Wei Li and Han Xu from Dr. Xiaole Shirley Liu's lab at Dana-Farber Cancer Institute/Harvard School of Public Health, and is maintained by Wei Li lab at Children's National Medical Center. We thank the support from Claudia Adams Barr Program in Innovative Basic Cancer Research and NIH/NHGRI to develop MAGeCK.

This is a sophisticated & integrated simulation and analysis environment for dynamical systems models of physical systems (ODEs, DAEs, maps, and hybrid systems). It supports symbolic math, optimization, continuation, data analysis, biological apps...

DeDAY (Demography Data Analyses) is a tool of analyzing demography data. It supports Gompertz, Weibull and Logistic distributions. DeDay also supports mixed mortality models based on these distribution such as the Gompertz-Makeham distribution. Distributions such as Gompertz describes only age-dependent mortality, which increases over time. Mixed mortality models, such as in Gompertz-Makeham distribution, consider a more general case where mortality is consist of both age-dependent and in-dependent mortality. Mixed models partition mortality into exogenous and endogenous components, so that the intrinsic survivorship can be estimated without the interference from extrinsic noise. DeDAY supports both interval-censored data and exact event-time data. Using MLE (Maximum Likelihood Estimate), DeDAY fits statistic model to the data. DeDAY also calculates the variances and the multi-dimensional confidence limits of model parameters. DeDAY is free for academic users.

The new version of MinimPy (MinimPy2) is available for download at: https://osdn.net/dl/minimpy2/MinimPy2.zip Please send your feedback about this new version to mahmood.saghaei@gmail.com (include MinimPy2 in the subject) ============================================================ MinimPy is a desktop application program for sequential allocation of subjects to treatment groups in clinical trials by using the method of minimization. Comprehensive reference help is available at http://minimpy.sourceforge.net MinimPy has been fully described in the following article: Saghaei, M. and Saghaei, S. (2011) Implementation of an open-source customizable minimization program for allocation of patients to parallel groups in clinical trials. Journal of Biomedical Science and Engineering, 4, 734-739. doi: 10.4236/jbise.2011.411090. Available at: http://www.scirp.org/journal/PaperInformation.aspx?PaperID=8518

This will be a place to release tools that have not yet been added to SciPy (or will not be added for whatever reason). Currently an interface to ImageMagick is here.

ptsa (pronounced pizza) stands for Python Time Series Analysis. A python module specifically designed with neural data in mind (EEG, MEG, fMRI, etc...), but applicable to almost any type of time series.