Parallel Processing for Next-Generation Sequencing (NGS) Analysis
High-throughput next generation sequencing (NGS) technology has quickly emerged as a powerful tool in many aspects of biomedical research. However, along with its rapid development, the data magnitude and analysis complexity for NGS far exceed the capacity and capability of traditional small-scale computing facilities, such as multithreading algorithms on standalone workstations. To address this issue, here we present a solution using the ever-increasing supply of processing power by massive parallel processing (MPP) systems.
Generic toolbox of Particle Swarm Optimization developed in Scilab (PSOTS). It is developed for a variety of complex problems, including single and multi-objective optimization problems, continuous and discrete problems, and mixed integer problems.
Syntactic is a simple C++ library for constructing general Neural networks. For now the library supports creation of multi layered networks for the Feedforward Backpropagation algorithm as well as Time Series Networks. More will be implemented soon.
A Compressed Suffix Arrays Based Index with Succinct LCP Information
We have moved our project to github. https://github.com/saaddan/Compressed-Enhanced-Suffix-Array
a framework library with a template method interface and inheritable classes for an executable process design which produces an executable which is both a GUI and a console application. It provides multi-threading for work items of the provider process .
It's an implementation of the A* algorithm together with a grid processor which pre-processes 8-bit bpm graphic files using a variable resolution and an SDL user interface to test it.
Toolkit for Automatic Control and Dynamic Optimization
ACADO Toolkit is a software environment and algorithm collection for automatic control and dynamic optimization. It provides a general framework for using a great variety of algorithms for direct optimal control, including model predictive control, state and parameter estimation and robust optimization. ACADO Toolkit is implemented as self-contained C++ code and comes along with user-friendly MATLAB interface. The object-oriented design allows for convenient coupling of existing optimization packages and for extending it with user-written optimization routines.
This is an Ada implementation of the Dancing Links X Algorithm as in Donald E. Knuth paper. AdaDLX is used to solve the Eight-Queens puzzle, Sudoku grids and Blocs in Box puzzle.
A new efficient and sensitive algorithm for mapping the new sequenced reads from next-generation DNA sequencing technologies to the genome assembly.
"Blue Planet" is a research project simulating the behaviour and darwinian evolution of unicellular lifeforms, each controlled by its own genetic program. Moreover, "Blue Planet Inhabitants" are suited for swarm intelligence and swarm research.
That project (RMOL) aims at giving developers concerned by the Revenue Management arena a library delivering a reference implementation for most of the published algorithms and methods. That library is intended to be used in simulated environment: it does not intend to be used in real world production systems.
The mathematical morphology have different applications on Image processing, it represent one processing non lineal sample. We show the CIDEFORM software as result of all mathematical morphology techniques.
Crybt is a Data-Encryption-Tool. You can use it easily for Dropbox.
Crybt is based on the Rijandael algorithm (AES). You can use it to encrypt your sensitive files direct into your Dropbox. But you can also use it for normal file-encryption. Crybt works with a new algorithm built by me ,that allowes you to save your password almost uncrackable.
CthughaNix is the reincarnation of Cthugha-L, a Linux port of one of the first audio visualization software packages, known as "An Oscilloscope On Acid".
Framework for developer Delphi
firstname.lastname@example.org Framework complete for developer quick and easy using the programming model by layers Model view presenter (MVP) having superclasses already being ready all actions database, persistence, validations, instance classes and layouts.
Visual C++ Utility Library
* EpLibrary project in this site is not maintained anymore. * The project has been moved to https://github.com/juhgiyo/EpLibrary EpLibrary is a utility library for Visual C++. The features includes: - Math Framework - Enhanced Binary Search - Sort - Stream Framework - Container Framework - Simple Debugger Framework - FileSystem Framework - Other Frameworks - Server/Client Template Framework - System Framework - Thread System For detailed documentation, please download this full document (EPLibrary Documentation.chm) from the "Downloads" Section. * If the documentation file is not visible after finishing download. Solution 1. ** Double-click the .chm file. ** In the Open File-Security Warning dialog box, click to clear the Always ask before opening this file check box. ** Click Open. Solution 2. ** Right-click the CHM file, and then click Properties. ** Click Unblock. ** Double-click the .chm file to open the file.
ESTReMo is an evolutionary simulation of transcriptional regulatory motifs. Our goal is to simulate the evolution of transcription factors and their binding sites in order to gain insight into the behavior of genetic regulator systems.
Provide geneology information, contact information, personal descriptions and webpages, calendars, etc in a web interface. This system will use php and any database system and will provide various level of public and private access.
Fast AFM force curve peaks detector algorithm
This is showcase program, with source code and sample data included for fast peak detection algorithm. It is great tool for entry level, automated analisys, to discard empty and junk curves and save only ones matching required criteria. Assuming that only 1% of data is worth reviewing, and that manual selection takes approx. 3 seconds per curve, you can save up to 8 hours per every 10000 curves (like 2 days every week!). Force amplitude analisys for single curve takes from 1 to 4 milliseconds on low-end intel dual core. Algorithm is so simple, that you can implement it in any language in few hours, without any specialized libraries. To be implemented in our Nanopuller AFM control software as real-time module. Requires LabVIEW Runtime engine to run .exe or LabVIEW 2013 for code.
Fiona is a tool to automatically analyze the interactional behavior of a given oWFN. It provides two techniques: it checks for the controllability of the given net by computing the interactiong graph and it calculates the operating guideline for the net.
This project uses massively parallel Graphics Processing Units(GPU) for neural network(Backpropagation) purposes.
This project aims to create an open source genetic algorithms (GA) library for the IBM Cell BE processor. A well-documented implementation of GAs is provided, along with a number of sample fitness functions illustrating how to use the GA library.
Open Source IM and voice client using Jabber and SIP protocols, with great audio quality thanks to speex and a nice and clean interface. Programmed in Java and C++. It supports chat, voice and file transfers.
Hyperspectral and Medical(MRI) data processing/compression tools using CORDIC based modules.
Individual Synaptic Activity Detection (ISAD)
ISAD is a peak detection software that detects individual (pre-)synaptic activity in microscopy images from neuronal cultures transfected with pHluorin. It computes synaptic signals from automatically segmented regions of interest and detects peaks that represent vesicle fusion events, thus, pre-synaptic activity. ISAD is based on MWA, which is a continuous wavelet transform based algorithm that employs multiple wavelets and is published as: Sokoll, S., Tönnies, K., and Heine, M. Detection of Spontaneous Vesicle Release at Individual Synapses Using Multiple Wavelets in a CWT-Based Algorithm. Med Image Comput Comput Assist Interv (MICCAI). 2012;15(Pt 1):165-72 ISAD is written in MATLAB and comes with a graphical user interface.