Open Source Python Scientific/Engineering Software - Page 31

SAGE is a free and open source mathematics software available from http://www.sagemath.org. The latest version (as of Jan 2012) is 4.7. Please do NOT download the much older version from sourceforge!

The scikits.timeseries python module provides classes and functions for manipulating, reporting, and plotting time series of various frequencies. The focus is on convenient data access while leveraging the existing functionality in numpy.

A compiler wrapper and a set of editor plugins allowing you to easily use Greek letters, accents, and other Unicode symbols in any programming language.

timecalc is a simple cli reverse-polish time calculator with dc-like synthax

This project has been moved to https://github.com/fmipp/trnsys-fmu This open-source project provides a stand-alone tool for exporting FMUs for Co-Simulation from TRNSYS 17 models. The current release supports FMI version 1.0 and 2.0. Instructions on installation and usage are given in the documentation, which is provided as part of the download. This documentation also contains a tutorial on how to export a TRNSYS model as FMU for co-simulation and how to link it with a simple controller implemented in Modelica. The tool is based on code from the FMI++ library.

Part-of-speech tagging is the task of assigning symbols from a particular set to words in a natural language text. ACOPOST implements and extends well-known machine learning techniques and provides a uniform environment for testing.

ATpy (Astronomical Tables in Python) is a Python module aimed at dealing with tables of astronomical data with a common API. To date, the following formats are supported: FITS, VO, and IPAC tables, and SQLite, MySQL, and PostgreSQL databases

Augustus development has moved to google code. The new project page is augustus.googlecode.com. New releases of the project are not currently being released to sourceforge. Augustus is designed for statistical and data mining models and produces and consumes models with 10,000s of segments. Versions of Augustus support PMML 3, 4.0.1, and 4.1.

We here present a novel computer algorithm, called AutoClickChem, capable of performing many click-chemistry reactions in silico. In silico modeling of click-chemistry products may prove useful in rational drug design and drug optimization.

Br-Gogo is a Brazilian open-source version of the Gogo Board project. Developed by CTI, a Brazilian research center. **<div class="sf-root" data-id="250926" data-badge="oss-users-love-us-white" style="width:125px"> <a href="https://sourceforge.net/projects/br-gogo/" target="_blank">Br-Gogo</a> </div>**

This is a testbed for projects of personal interests, especially academic projects.

BrennerMD is a public domain Fortran molecular dynamics program by Donald Brenner and other people. This project is to maintain the original source code and to build a Python interface on top of it.

CitySpeed is a Python package that uses online mapping services to gather statistics on the efficiency and complexity of road networks. This can be used to create maps showing how fast you can drive around a particular city.

This advanced machine learning algorithm is a Michigan-style learning classifier system (LCS) developed to specialize in classification, prediction, data mining, and knowledge discovery tasks. Michigan-style LCS algorithms constitute a unique class of algorithms that distribute learned patterns over a collaborative population of of individually interpretable IF:THEN rules, allowing them to flexibly and effectively describe complex and diverse problem spaces. ExSTraCS was primarily developed to address problems in epidemiological data mining to identify complex patterns relating predictive attributes in noisy datasets to disease phenotypes of interest. ExSTraCS combines a number of recent advancements into a single algorithmic platform. It can flexibly handle (1) discrete or continuous attributes, (2) missing data, (3) balanced or imbalanced datasets, and (4) binary or many classes. A complete users guide for ExSTraCS is included. Coded in Python 2.7.

PROFESSIONAL HYDRAULIC CALCULATIONS A reliable engineering application created for designers, mechanics, and machine technicians. Perform precise technical calculations instantly, completely securely, and without ads.

NOTE: The Inelastica project moved to https://github.com/tfrederiksen/inelastica/ in February 2018. Pre- and post-processing tools for SIESTA (DFT, quantum chemistry) and TranSIESTA (quantum transport): (1) Calculate phonon frequencies, e-ph couplings, and inelastic contributions to the conductance (IETS). (2) Access Hamiltonian etc from Python. Some code documentation and installation instructions are available at this mediawiki page: http://dipc.ehu.es/frederiksen/inelastica/index.php.

Platform for parallel computation in the Amazon cloud, including machine learning ensembles written in R for computational biology and other areas of scientific research. Home to MR-Tandem, a hadoop-enabled fork of X!Tandem peptide search engine.

KEMP is a fast FDTD solver on a GPU-based cluster. The FDTD (Finite-Difference Time-Domain) method is a popular numerical method for electromagnetic field simulations. KEMP enables hardware accelerations suitable for multi-GPU, multi-core CPU and GPU cluster. KEMP also provide easy configuration by using Python scripting language.

Liegkat-Archiv delivers ALK converters for spatial data formats (EDBS, BGRUND, SQD, DFK, HK) and coordinate systems used in German cadastral agencies before ALKIS into KML and JML. It delivers Python packages and XSL files.

LightProfiler – application for performance analysis of the Oracle databases. It generates detailed resource profile for extended SQL trace files (10046 event), containing information about consuming of response time (by events, by cursors, etc.), data files usage, error analysis (SQL, PL/SQL) and much more. Also it contain tools for additional processing of trace files (extract session data, splitting files) and for management of database's sessions (disconnecting, tracing, monitor parameters, blocking locks, events and etc.)

LymPHOS2 is a web-based Application at www.LymPHOS.org containing peptidic and protein sequences and spectrometric information on the PhosphoProteome of human T-Lymphocytes. - Nguyen, TD., Vidal-Cortes, O., Gallardo, Ó., Abian, J., Carrascal, M., LymPHOS 2.0: an update of a phosphosite database of primary human T cells. Database 2015, 2015. DOI: 10.1093/database/bav115 - Carrascal, M., Ovelleiro, D., Casas, V., Gay, M., Abian, J., Phosphorylation analysis of primary human T lymphocytes using sequential IMAC and titanium oxide enrichment. J. Proteome Res. 2008, 7, 5167-5176. DOI: 10.1021/pr800500r - Ovelleiro, D., Carrascal, M., Casas, V., Abian, J., LymPHOS: design of a phosphosite database of primary human T cells. Proteomics 2009, 9, 3741–3751. DOI: 10.1002/pmic.200800701 - Gallardo, Ó., Ovelleiro, D., Gay, M., Carrascal, M., Abian, J., A collection of open source applications for mass spectrometry data mining. Proteomics 2014, 20, 2275-2279. DOI: 10.1002/pmic.20140012

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

NLOPredict is a nonlinear optical prediction and data analysis tool. Nonlinear optical measurements can yield information about the structure of crystals, and orientation of molecules at surfaces and interfaces.

OpenSQUID is a Python framework for the control of SQUID (superconducting quantum interference device) readout electronics. It currently supports the Star Cryoelectronics PCI-1000 electronics with PFL-100 and PFL-102 flux-locked loops. Simultaneous operation of both PFL-100s and PFL-102s from a single PCI-1000 is supported. More features are under development. The software is implemented in Python and aims to be easily integrated with user-defined measurement and control code.