Open Source Java Scientific/Engineering Software - Page 51

This project has the role of simulating simple Curvilinear and Rectilinear Motions with an easy to use user interface. This program can be used for educational purposes as well as for any other purpose anyone would like. The executable file is a .jar files which means that it can run in any operating system that supports java. Above you can see a screenshot of the program while it is operating.

Cuttlefish aims to be a highly extensible visualization and analysis platform for all kinds of network data. IMPORTANT: The Cuttlefish project has been migrated to github: https://github.com/dev-cuttlefish/cuttlefish

CySBGN adds support to Cytoscape to import, export, visualize and analyse System Biology Graphical Notation (SBGN) maps.

Cyberinfrastructure Shell (CIShell) is an open source, community-driven framework/application for the integration and utilization of datasets, algorithms, tools, and computing resources. Algorithms can be integrated using most programming languages.

The Cybertory™ Virtual Molecular Biology Laboratory is an on-line virtual environment for conducting simulated experiments in molecular genetics.

Software suite for cell modelling

A lightweight and scalable genome browser

Cyclone is a Java application for quickly placing points on a 2D plan or in a form, in order to draw cyclone courses.

Cyclone aims at facilitating the use of BioCyc, a biological pathway tool. Cyclone provides a comprehensive library of Java classes.

The Cylindrical Alignment App is the successor to Cylindrical BLAST Viewer. Similarly, it arranges search or other comparisons, against their "axis". Searches can be made by Basic Local Alignment Search Tool, ClustalW, or Gene Machine to name a few. This version does not require downloading or installing Java3D, and has more modern GUI features.

3D viewer which arranges BLAST hits and other bioinformatics-related alignments in a rotating, cylindrical display. Feedback appreciated. NOTE: requires Java3d installation. Superceded by Cylindrical Alignment App

A Cytoscape plug-in to interface with R language. The connection is established using Rserve library.

Homepage: www.cellnopt.org Based on prior knowledge networks CellNOptR can derive functional information about the network using logic modeling. CytoCopteR is a friendly way to use CellNOptR taking advantage of the network visualization and analysis of Cytoscape and without requiring knowledge on R.

This project implements a Cytoscape plugin for viewing and manipulating pathway maps for metabolic models created by the Model SEED (http://www.theseed.org/models). See the "Files" area for README. See Project Homepage for Tutorial.

Cytoprophet is a Cytoscape plugin that helps researchers infer new potential protein (PPI) and domain (DDI) interactions. Users input a set of proteins and retrieve a network of plausible protein and domain interactions with a score.

Cytoscape is a software platform for computational biology and bioinformatics, useful for integrating data, and for visualizing and performing calculations on molecular interaction networks

D-Cog (Declarative-Cognition) is a Java based framework for training software components (reusable, object-oriented, interface-driven components). Instead of programmed, software components are trained by example to get the expected results.

D-finder is a bioinformatic search algorithm for the identification of D-sites in JNK interacting proteins. The algorithm is a combination of pattern matching and a hidden markov model (HMM) based on a training set of known JNK D-sites.

D.U.C.K (Determine segmentation of Unknown words by using Context Knowledge)is an NLP tool, which aims to find the correct segmentation for unknown words in written Hebrew. Statistics from different scopes will be used to determine the segmentation.

Eukaryotic gene expression is controlled through molecular logic circuits that combine regulatory signals of many different factors. Complexation of transcription factors and other regulatory proteins is a prevailing and highly conserved mechanism of signal integration within critical regulatory pathways and enable to infer controlled genes as well as the exerted regulatory mechanism. We developed DACO (domain-aware cohesiveness optimization), a novel algorithm that combines protein-protein interaction networks and domain-domain interaction networks with the cluster-quality metric cohesiveness. The metric is locally maximized on the holistic level of protein interactions while sophisticated connectivity constraints on the domain level are utilized to account for the exclusive and thus inherently combinatorial nature of the interactions within such assemblies. The original publication can be found on http://bioinformatics.oxfordjournals.org/content/30/17/i415 .

Digital Archive and Retrieval Tool (DART) presents engineers with an easy to use alternative to typical SVN or other CVS type systems. It allows engineers to easily archive data and provides an interface for managing and accessing store information.

DASM is a new simple platform which helps programmer to implement and evaluate any distributed algorithm. Programmer can implement his/her distributed algorithm using DASM primitives and monitors the results in diagrams during execution.

DAWN is an open-source, agent-based urban water demand simulator. „

Learn words in german that you know at your own pace. With this system you can add the words you knew in a day and then do exercises with them. Written by: Jovanny Pablo Cruz Gómez. Computer Engineering Student. IPN, ESIME Culhuacan, Mexico City.