Energy Based Multiple Sequence Alignment (MSA) for Binding Sites
Multiple Sequence Alignment for Transcription Factor Binding Sites using Di nucleotides dependencies and relying on Free Interaction energies between neighbouring DNA bases to stabilise substitution energy of the alignment. http://www.ncbi.nlm.nih.gov/pubmed/23990411
A personal coder keys applied to developement nuk friendly for
A simple sieve/prefactor program for Eisenstein-Mersenne Primes
A simple sieve/prefactor program for the so-called Eisenstein-Mersenne Primes: 3^p +- 3^((p + 1)/2) + 1. See http://oeis.org/A125738, A125739 and  for a good introduction. Some easily established properties are: p must be prime; sign is minus for p=+-1 (mod 12), plus otherwise; composites only have factors of form 6kp+1 (integer k). Related probable primes (3^p -+ 3^((p + 1)/2) + 1)/7 are sieved at the same time. See http://oeis.org/A125743, A125744. After sieving, the Berrizbeitia-Iskra or a Proth test can be run; this is best implemented with FFT mod (3^3p+1) using GWNUM library. A sample implementation (a patch to the LLR program) is available from Batalov.  P.Berrizbeitia B.Iskra, 2010; http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.189.311  OEIS: http://oeis.org/
An evolutionary simulator of transcription regulatory networks
ESTReMo is a genetic algorithm-based simulator to explore the evolution of transcription factors and their binding motifs on realistic genomic backgrounds.
ETHNOS - Expert Tribe in a Hybrid Network Operating System
The ETHNOS environment is composed of: 1) ETHNOS-6, a dedicated distributed real-time operating system (developed as an extension to Linux), from which the overall environment takes its name, supporting different high level representation, communication, and execution requirements, 2) a dedicated network protocol designed for both the single robot and the multi-robot environment, specifically designed for noisy wireless communication, 3) an object oriented Application Programming Interface (API) based on the C++ language (and a subset based on Java), 4) a set of additional development tools (a robot simulator, a Java-applet template, etc.). Check the official website for a Reference Manual.
ROS node to control LEGO MINDSTORMS EV3
- Java SE 1.7 compatible - Can be run on both Windows/Linux PC - Can be run on Android devices(Tested on ASUS fonetab7, ASUS zenfone4, Samsung Galaxy S4) - Can be run on reflashed ARM-based AndroidTV sticks (Tested on MK808) - No custom firmware for EV3 brick - Supports about 15 EV3/NXT/HT sensors - Supports EV3 & NXT motors - Supports Android camera
Wave Audio copy based on a background image.
TWD: Tracing Wave Drawing is a tool used to copy using Bezier curves one audio wave based on a background image then export data to floating point or Wav Audio. The bezier curves generated data "," floating that are stored in a text box are the coordinates of each segment consisting of the waveform, only in this way can be exported waveform copied and import it into another instrument hardware or software .. You can also experiment with TWD since not only limited to the field of Audio, but also by the coordinates of 'floating, you can program in cycles innumerable factors in Robotics. this is just an idea of what you can get with TWD
Modular CNC software for Arduino controller
The goal of the project is the realization of a modular firmware that allows to control a CNC machine with different utensils. For instance, a CNC with a drill, with few changes can become a plotter with a pen or cutting machine to cut cardboard or stickers. In order to do that, we want project a CNC router with a mechanism that allows a fast utensil change and a controlling firmware which can use different utensils changing some configuration parameters.
Modélisation prospective 2050 sur les énergies
Ecotype, au delà d’un jeu, est un outil de modélisation du territoire, adapté à l’échelle de la commune sur laquelle s’inscrit l’événement et qui permet d’intervenir sur les divers paramètres qui président au développement d’un territoire : élaboration du zonage, définition des Coefficients d’Occupation des Sols, mise en place des infrastructures et équipements publics en corrélation avec le PLU de la commune … La modélisation prospective —un outil scientifique des plus sérieux— permet de visualiser les conséquences de ces choix, tels qu’opérés à l’échelon local, sur l’ecosystème planétaire global et ce, sur une échelle de 50 ans. Le modèle algorithmique d’Ecotype a été développé par le CMA (Centre de Mathématiques Appliquées), l’un des quatre centres de recherche de MINES ParisTech (École des Mines de Paris) implantés à Sophia-Antipolis, dont la réputation n’est plus à faire dans le domaine de la modélisation.
This is a Java implementation of Edmonds' Algorithm (Chu-Liu Algorithm) for finding maximum branchings in a directed graph.
Implementation of the finite element method for linear elasticity
Code for solving linear elasticity problems using the finite element method. Current features -Handles complex geometry and boundary conditions -Linear triangle and quadratic quad elements -Sparse matrix CG solver -MPI Parallelism -GMSH Input -VTK Output
Lexicon and data model for Elvish languages
A lexicon of Tolkien's Elvish languages, backed by an XML data model of the lexicon's contents. This project has been migrated to Github: https://github.com/pfstrack/eldamo
A simple (but growing) calculator for many electronic laws
This is a compilation of applications that have been made into one package, all of the programs included have been created by me, i have included a few simple law calculators at the moment, but will add more throughout updates. The current build includes: • Leyden Jar Capacitance Calculator • Resistor Colo(u)r Coder And more!
An electromechanical computer simulation.
This project is a simulation of an electromechanical computer based upon the design presented in Charles Petzold's book "CODE: The Hidden Language of Computer Hardware and Software"
A tutorial Galerkin meshfree code
Meshfree or meshless methods were born to replace the traditional finite element in applications where meshing a complex geometry and/or excessive remeshing is involved. This code, written by Vinh Phu Nguyen, implements one and two dimensional Element Free Galerkin (EFG) method which is one of the most common meshfree methods for elasticity. It also implements Partition of Unity based enrichment for weak and strong discontinuities. The method and the implementation are described in the following article Meshless methods: a review and computer implementation aspects VP Nguyen, T Rabczuk, S Bordas, M Duflot, Mathematics and computer s in simulation 79 (3), 763-813.
Solving and graphing mathematical equations
Equation Untie is an equation solver that enables you to solve and graph mathematical equations of the first and second degree in both real and complex planes.
Program that compares AISC sections with those found in Ecuador
The AISC steel construction manual provides handy solutions for designing steel members, but the sections provided within the manual are rolled in compliance of AISC standards, only useful within the U.S.. This program is for the steel designer that works in Ecuador and uses the AISC Steel Construction Manual. After desingning the structure and selecting the apropiate sections, this tool checks for the most similar sections available within the ecuadorian market
A small parser for the Esperanto language, intended as an API for other programs. The blog entry describing this program's function and motivation can be found here: http://coder32768.blogspot.com/2014/04/gort-klaatu-barada-esperanto.html The program takes text in Esperanto, and returns an object graph describing that utterance. The program has expansion points for transforms of this graph, in the spirit of transformational grammars.
Targeting Speed Calculator for Eve Online
Calculates Targeting speed from Scan Resolution and Signature Radius Signature Analysis is calculated as lvl5 Sensor Booster calculated as t2 with Scan Resolution script Sensor Amplifier calculated as t2
A pipeline to extract novel cassette exons/retained-introns
ExonFinder provides a pipeline to extract novel cassette exons and novel retained-introns from the results of mapping cross-species ESTs against a target genome via blat.
A markup language designed to capture science data and its context
The Experiment Markup Language (ExptML) is a markup language, in XML, designed to store all the data and metadata (context) from all parts of the scientific process. The format has a central schema that is used by a schema set that defines 26 different datatypes that are the building blocks of what scientists do when they do experiments in a laboratory.
Connected Component Labeling Algorithm - Extracting Objects From image
fast Connected Component Labeling Algorithm - java application - Extracting Objects From image
A middleware that exposes a single API for eye-tracking systems
This is an SDK that unites input from various eye-tracking systems and provides a common API for developers regardless of the system in use.
JSON based text search Java Project
----------------- - What is it? - ----------------- The "Falcon Search" is a JAVA API and tool to search inside the documents. It was originally started to search the content in pdf files under the project "HAWK Search". Searching with this tool is query-based not word-based as in most of the document search tools OR document readers. It also takes care of jumbling of words within query and spelling mistakes. Commonly used techniques in this project are Natural Language Processing, Information Extraction and Question-Answering Architecture. ---------------------- - Latest Version - ---------------------- Details of latest version can be found on project website - http://geekdadaji.com --------------------------- - CONTACT DETAILS - --------------------------- CREATOR : SWAPNIL A JADHAV (saj1919) EMAIL ID : firstname.lastname@example.org WEBSITE : http://geekdadaji.com LICENSE : CC BY-NC 4.0
NGS data characterization and in silico read generation
FASTQSim is a tool that provides the dual functionality of Next-Gen Sequencing dataset characterization and metagenomic data generation. FASTQSim is sequencing platform-independent, and computes distributions of read length, quality scores, indel rates, single point mutation rates, indel size, and similar statistics for any sequencing platform. To create training or testing datasets, FASTQSim has the ability to convert target sequences into in silico reads with matching error profiles. FASTQsim allows the user to simulate individual read datasets that can be used as standardized test scenarios for planning sequencing projects or for benchmarking metagenomic software. In this regard, in silico datasets generated with the FASTQsim tool hold several advantages over natural datasets: they are sequencing platform independent, extremely well characterized, and less expensive to generate.