Open Source Perl Scientific/Engineering Software - Page 5

The Khepera III Toolbox is a collection of scripts, programs and code modules for the Khepera III robot. It allows for easy access to all sensors and actuators of the robot and provides a lot of standard programs.

Kriterion is a document retrieval and categorization engine capable of full text searching. There is no need for keyword or context-based information.

Software from LoCI Laboratory is devoted to information logistics, the study of the flexible coscheduling of the physical resources that underpin computer systems: storage, computation, and data transmission. We use IBP, L-Bone, exNode and LoRS.

Cap analysis of gene expression (CAGE) is a sequencing based technology to capture the 5’ ends of RNAs in a biological sample. After mapping, a CAGE peak on the genome indicates the position of an active transcriptional start site (TSS) and the number of reads correspond to its expression level. CAGE is prominently used in both the FANTOM and ENCODE project. MOIRAI is a compact yet flexible workflow system designed to carry out the main steps in data processing and analysis of CAGE data. MOIRAI has a graphical interface allowing wet-lab researchers to create, modify and run analysis workflows. Embedded within the workflows are graphical quality control indicators allowing users assess data quality and to quickly spot potential problems. MOIRAI package comes with three main workflows allowing users to map, annotate and perform an expression analysis over multiple samples.

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.

We developed a novel clustering-free method, microarray-associated motif analyzer (MAMA), to predict novel cis-acting elements based on weighted sequence similarities and gene expression profiles in microarray analyses. Simulation of gene expression was performed using a support vector machine and based on the presence of predicted motifs and motif pairs. The accuracy of simulated gene expression was used to evaluate the quality of prediction and to optimize the parameters used in this method. After optimization, MAMA accurately simulated more than 87% of gene expression. See Kakei Y, Ogo Y, Itai RN, et al. (2013) Development of a novel prediction method of cis-elements to hypothesize collaborative functions of cis-element pairs in iron-deficient. Rice 6(1): 22.

MoViT is a distributed software suite for the virtualization of mobile wireless networks. MoViT provides researchers and developers with a virtualized environment for developing and testing mobile applications and protocols for any hardware and software platform that can be virtualized. The distributed nature of MoViT allows for the emulation of mobile networks of arbitrary size. Additionally, the network connectivity is shaped transparently such that the connectivity observed by each virtual node resembles that of a physical mobile network.

Mobilemaps is a Nearby Engine which allows users to find Web pages by location. Extremely fast and capable of scaling to any number of pages, it supports OpenGIS map-servers and uses MySQL, Perl and C.

NDAD is the UK National Digital Archive of Datasets. This project contains the source code for the bespoke software which drives the public website and many aspects of the data curation/archiving process.

The purpose of the project is moving large-size of biological database and FASTA computation onto wide area network by leveraging distributed computation-enabled storage developed for the field of logistical network.

Neurospaces is a development center for tools in computational neuroscience. See http://www.neurospaces.org/

This is a unix distribution I made so that I can develop from anywhere--a virtual desk if you will. Some of my friends and colleagues have found it useful, and an easily accessible place to put the operating system up is on the internet.

A modular, database-backed system for 5 dimensional (5D) analytical biological microscopy and cell-based screening. Please note - we have moved. Please come visit us and download from our new site at http://cvs.openmicroscopy.org.uk

The Open Source Space Flight Dynamics (OSSFD) project is intended to provide the community with an open source solution to space flight dynamics.

This project is a reference, open source implementation of the coordinate conversion algorithms for the Polish geobotanical grid called ATPOL.

Project moved to https://github.com/ivandeex/optikus

Smart servers that can provide customized snippets of digital orthophotos using just-in-time geoprocessing and interoperable web-based components. These servers are based on the MITOthoServers who was under the GNU Public License (GPL).

Ozitools project aims to collect/create a set of tools for OziExplorer map processing and convertion to/from open formats (e.g. GeoTiff) appropriate for using in GIS applications.

Statistics modules in Perl Data Language, with a quick-start guide for non-PDL people. They make the PDL shell work like R, but with PDL threading (fast automatic iteration) of procedures including t-test, linear regression, and k-means clustering.

This project contains a custom version of the GROMACS molecular dynamics software package that helps users to choose parameters for the PME electrostatics model which produce a known error in the PME approximation for minimal computational cost.

Diversity assessments and comparisons of large compound databases require calculating similarities of millions of compounds in an affordable time. ParaSim addresses this challenge by parallelizing the calculations according to the number of computing cores available on a single machine. It is optimized for the throughput of very large numbers of query structures against very large numbers of reference structures. As as special feature, ParaSim allows to store and and to access frequently queried datasets as persistant objects in memory for short response times. ParaSim calculates chemical similarities based on binary structural fingerprints. It does not compute fingerprints by itself but relies on third party software to do so. Basically, all types of structural fingerprints which can be stored in an array of bits (a bitset) can be used by ParaSim. See the Wiki (https://sourceforge.net/p/parasim/wiki/Documentation/) for detailed documentation. FEEDBACK HIGHLY APPRECIATED!

Comprehensive & high performance data distribution &transformation system. Features a simple, user-friendly event driven scripting interface transparently generates & execs highly efficient Perl/C code. Uses:ETL,datawarehousing,statistics,data-cleansing.

**** This page is not used for this project any longer. *** Please update your bookmarks and go to https://github.com/UUPharmacometrics/PsN

Basic implementation of K-nearest neighbour Algorithm and the application of KNN to classify protein sequences as transmembrane beta barrel or non-transmembrane beta barrel on the basis of whole sequence amino acid composition given as input.

The goal is to use distributed computing in the least bandwidth-intensive way to find a large prime number. We will have four parts to the project.