Medical Image Registration Library
SimpleElastix is an extension of SimpleITK that comes with the elastix C++ image registration library. This makes state-of-the-art medical image registration really easy to do in languages like Python, Java, C# and R.
Viewmol is a graphical front end for computational chemistry programs. It is able to graphically aid in the generation of molecular structures for computations and to visualize their results.
Long read to rMATS
lr2rmats is a Snakemake-based light-weight pipeline which is designed to utilize both third-generation long-read and second-generation short-read RNA-seq data to generate an enhanced gene annotation file. The newly generated annotation file could be provided to rMATS for differential alternative splicing analysis.
This is a simple encryption tool to work with home-grown encryption algorithms. It can run as either a GUI, a command-line application, or a network proxy.
This application provides a web based visual browser for NetCDF files. The application provides a simple and friendly user interface for getting a quick overview of the data contained in the files.
Computational electromagnetics software. Uses surface Method of Moments, enhanced by using the Multilevel Fast Multipole Method. Code is parallelized and runs on laptops, desktops and clusters. The code precision is adjustable, it is fast and uses little memory. CFIE is used for closed surfaces, and EFIE for open PEC surfaces. Can function on GMSH, GiD and ANSYS meshes.
A Python computer vision library
PyVision is a object-oriented Computer Vision Toolkit for researchers that contains vision and machine learning algorithms and algorithm analysis and easily interfaces with scipy/numpy, PIL, opencv and other computer and machine learning libraries.
Python module for creating functions computing the Cyclic Redundancy Check (CRC). Any generating polynomial producing 8, 16, 24, 32, or 64 bit CRCs is allowed. Generated functions can be used in Python or C/C++ source code can be generated.
Portable Plot is a pure ansi/iso c++ plot library that makes the construction of native plot widgets easy.
A FDTD solver for electromagnetic wave simulations on a GPU cluster
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.
A module containing python wrappers for the SUite of Non-linear DIfferential/ALgebraic Solvers (SUNDIALS), using ctypes.
An open source malware analysis tool
Zero Wine Tryouts is an open source malware analysis tool. Just upload your suspicious file (e.g. Windows executable file, PDF file) through the web interface and let it analyze. For more information, please visit project website: http://zerowine-tryout.sourceforge.net/
cclib is an open source library, written in Python, for parsing and interpreting the results of computational chemistry packages. It currently parses output files from ADF, Firefly, GAMESS, GAMESS-UK, Gaussian, Jaguar and ORCA. IMPORTANT! As of version 1.2, cclib development has moved to github. Please use the flowing pages for up-to-date information about cclib: Repository (source code, tracker) - https://github.com/cclib/cclib Online documentation - http://cclib.github.io/
RNNLIB is a recurrent neural network library for sequence learning problems. Applicable to most types of spatiotemporal data, it has proven particularly effective for speech and handwriting recognition. full installation and usage instructions given at http://sourceforge.net/p/rnnl/wiki/Home/
RNA coding potential assessment tool
Using RNA-seq, tens of thousands of novel transcripts and isoforms have been identified (Djebali, et al Nature, 2012 , Carbili et al, Gene & Development, 2011) The discovery of these hidden transcriptome rejuvenate the need of distinguishing coding and noncoding RNA. However, Most previous coding potential prediction methods heavily rely on alignment, either pairwise alignment to search for protein evidence or multiple alignments to calculate phylogenetic conservation score (such as CPC , PhyloCSF and RNACode ). This is because most previously identified transcripts including protein coding RNA and short, housekeeping/regulatory RNAs such as snRNAs, snoRNA and tRNA are highly conserved. While still very useful, these approaches have several limitations: Most lncRNAs are less conserved and tend to be lineage specific which greatly limit the discrimination power of alignment-based methods. For example, of 550 lncRNAs detected from zebrafish, only 29 of them had detectable sequence
A database management system for ecological field surveys
ECOLOG is a specimen-based, cross-platform relational database management system, aimed at the storage, retrieval and preliminary analysis of data on sites, species, and specimens gathered in ecological field surveys and biodiversity inventories. The main goal of ECOLOG is to make the data gathered in ecological field surveys readily accessible, providing lists of species collected in the study area and informations on habitat preferences, abundance or rarity of a given species, biometrics, morphology, dominance, and spatial location of each specimen collected in the field.
Evolutionary Genetics and Genomics Library
EggLib has moved to http://mycor.nancy.inra.fr/egglib/ since version 3.0.0.
IFEFFIT is a library and set of interactive programs for the analysis of x-ray absorption fine-structure (XAFS) data. IFEFFIT combines state-of-the-art analysis algorithms with graphical display of XAFS data, and general data manipulation. It can be
Analyze molecular simulation data
LOOS is a light-weight object oriented software library for creating new tools for analyzing molecular simulation data, written in C++. The main design goal is to allow casual programmers to easily implement new analysis methods.
Configurable Editor in Python
PyEdit is a fully featured fast text editor written in Python. It can be used in any platform that has GTK. Because it is written in Python, it is easily configurable. Features code spell check and macro recording. Tested in Win/Lin/Mac --- Update: Using the editor full time V23 is mature enough for production --- Update: Had to downgrade to PyGTK 2.22.xx as 2,24,x had a double click message bug. (uploaded 22.2 to this project) --- Update: V33 is working as a champ. New features, tablet like drag ..
Queequeg is an English grammar checker for non-native English speakers.
Theoretical Density, Orbital Relaxation and Exciton analysis
The TheoDORE (Theoretical Density, Orbital Relaxation and Exciton analysis) package is a general purpose program suite for the analysis of excited states obtained from quantum chemical excited state calculations. Wavefunction analysis is based on state and transition density matrices, which provides a unified formalism applicable independent of the wavefunction model. TheoDORE is interfaced to a number of quantum chemical programs (Q-Chem, Columbus, Turbomole) and can be used for a wide range of excited state methods (MR-CI, ADC, CC, TDDFT). It is written in a modular fashion to allow for an easy extension of these capabilities.
LaTeX2WP converts a document written in LaTeX into a form suitable to be cut and pasted into the WordPress online editor.
A high-level python to matlab(tm) bridge. Let's matlab look like a normal python library.
RNA editing detection by NGS data
REDItools are python scripts developed with the aim to study RNA editing at genomic scale by next generation sequencing data. RNA editing is a post-transcriptional phenomenon involving the insertion/deletion or substitution of specific bases in precise RNA localizations. In human, RNA editing occurs by deamination of cytosine to uridine (C-to-U) or mostly by the adenosine to inosine (A-to-I) conversion through ADAR enzymes. A-to-I substitutions may have profound functional consequences and have been linked to a variety of human diseases including neurological and neurodegenerative disorders or cancer. Next generation sequencing technologies offer the unique opportunity to investigate in depth RNA editing even though no dedicated software has been released up to now. REDItools are simple python scripts conceived to facilitate the investigation of RNA editing at large-scale and devoted to research groups that would to explore such phenomenon in own data.