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This is a collection of different little tools written in MATLAB, JAVA, Python. They all have to to do with Imaging & Microscopy for life science research and related topics or problems. Some of them are meant to be used with ImageJ and MicroManager.
A simple messaging system designed for rapid deployment on robotic platforms. Based on the venerable Inter-Process Communication Package, simpleIPC offers several key extensions: units, auto-discovery, message descriptors, and a Python wrapper. See Soto.
Collection of wrappers for textile composite modelling package TexGen and a variation of structural FEA packages (baseline being Calculix) to allow extraction of 3D mechanical property data.
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Investigation the concept of speed knowledge acquisition through speed reading and visual display. The initial version should be based on the concept provided by Dictator and should be a variable speed reader, handling TeX formatted files. Project design
Python-accessible toolkit for Geoscience & Remote Sensing Applications
GeoSciPy is a set of C and Python functions that provide an API for all aspects of Geoscience and Remote Sensing Applications.
Functions include reading/writing of many data formats, images, vectors, ..., and processing of images, vectors, ... including map projections, ... The library is written C, using HDF5 as the file format for storage of all remotely-sensed data and ancillary data, as well as processed data.
Accelerometer-based wireless wind and rain sensor.
This is a university project that aims to create a partial weather sensor (rain + wind) using just one accelerometer (LIS302DL), a PIC (18f2520), two ZigBee 802.15.4 modules and a PC.
JSalesman is a very efficient Travelling Salesman problem solver that produces high-quality outputs. JSalesman uses hierarchial and multi-level approaches to solve the problem fast.
Maximal Clique Motif Reduction (MCMR) is a software program for running and then combining the output of multiple motif finder programs, such as MEME, AlignACE and Weeder, into a set of consensus predictions with associated confidence rankings.
...Its 'Cleanroom' applets allow codesmiths to access the lab environment, used to create semiconductors, substrate prototypes, chipset instruction blocks and other Labcoat projects. Our extensions in future releases will include UML support for C#/C++ conforming projects, import/export architecture schematics and refactoring sub-projects.
mgE3D - mgEngine3D is an unfinished 3D Engine based on OpenGL. By now
it provided several features like scenetree, mesh/skeleton mesh rendering and animation, terrain, materials, textures, multiple viewports, Python exporter for Blender and so on.
Python package OCFit includes 4 classes for analysis and fitting of O-C diagrams of Eclipsing binaries
In a case of using this package for scientific purposes, please, cite our paper Gajdoš &
Parimucha (2018) where you can also find more detail description about fitting functions
and used models.
For install it, download/clone this repository or download suitable binary file from releases.
Not working yet!
The 3D Slicer is freely available, open-source software for visualization, registration, segmentation, and quantification of medical image data. Follow the link for more info: http://slicer.org
trimAl can consider several parameters, alone or in multiple combinations, in order to select the most-reliable positions in the alignment. These include the proportion of sequences with a gap, the level of residue similarity and, if several alignments for the same set of sequences are provided, the consistency level of columns among alignments. Moreover, trimAl allows to manually select a set of columns and sequences to be removed from the alignment.
trimAl implements a series of...
Python module to interface mzML data in Python based on cElementTree with additional tools for MS-informatics.
CITATION
Please cite us when using pymzML for your publications.
Bald, T., Barth, J., Niehues, A., Specht, M., Hippler, M., & Fufezan, C. (2012).
pymzML - Python module for high throughput bioinformatics on mass spectrometry data.
Bioinformatics, 1-2. doi: 10.1093/bioinformatics/bts066