Open Source Java Scientific/Engineering Software - Page 48

Cloe (Closure Editor) is a graphical, Java based tool used for editing contigs, resolving contig features, and closing both sequencing and physical gaps.

Application for visualisation of Chromosomal LOcations of Gene Expression.

CloneAnalyzer is a tool for software quality analysis. It allows you to find, display and inspect clones, which are fragments of duplicated source code resulting from lack of proper reuse. It can be used as a plugin for Eclipse and on the command line.

Cloud-TM aims at defining a novel programming paradigm to ease the development and administration of cloud applications. It will develop a Self-Optimizing Distributed Transactional Memory middleware for distribution, persistence and fault-tolerance.

A map/reduce based application for mapping short reads generated by the next-generation sequencing machines.

A map/reduce based application for mapping short reads generated by the next-generation sequencing machines.

CloudBurst is a parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics.

CloudGPS is J2ME map application with following features: multiple maps, unlimited cache, show your location using GPS, geocoding and turn-by-turn navigation, record and replay NMEA, based on OpenStreetMap and CloudMade.

To reduce resource over and under-provisioning, software systems can be migrated to IaaS and PaaS-based cloud environments. However, aligning and optimizing existing software systems for a cloud computing foundation often involves substantial reengineering activities or at least an elaborated configuration during the migration. There exist various challenges that have to be addressed, for example, systematically comparing cloud environment candidates, checking the conformance with particular cloud environments, or simulating monitored workload for envisioned cloud-based target architectures to evaluate future costs. CloudMIG Xpress addresses those kinds of challenges and provides tool support for the comparison and planning phases to migrate software systems to PaaS or IaaS-based clouds. It originates from an academical prototype and is built to support research in cloud migration.

Cloudware is the software implementation of Cloudman, a peer-to-peer framework for gossip-based protocols. It includes services like peer sampling, aggregation, topology management, load-balancing, etc.

Clown is a "clustering" framework. It allows you to cluster datasets (in ARFF) format using a number of different clustering algorithms.

Comprehensive Meta Prediction and Annotation Services for Proteins: The new all-in-one prediction tool that can be easily extended to include any SOAP/WSDL-enabled prediction servers. A concise user interface lets you use the results instantly.

CoSMoSim offers an integrated framework for model development, simulation, & experimentation. Its unified logical, visual, and persistence framework supports specifying families of parallel CA, DEVS, Statecharts, and XML-Schema models (see DEVS-Suite simulator).

The co-simulation adapation platform serves as programming framework and middleware to enable coupling of distributed, heterogeneous numerical models. The framework facilitates the adaptation and integration of new sub-models into a common simulation platform.

Multilingual Content Synchronization with Wikis: CoSyne is a Research and Technological Development project co-funded by the European Union. Details: http://cosyne.eu

Goal of Coatie3D project is the development of a 3D graph drawer/ viewer. The purpose of graph drawing is the identification of a pleasant layout for a given graph.

CodeBot is a java (swing) based application that allows to generate keyboard and mouse events, by using simple scripting configuration. Bot allows to start and manage scripts in new threads. Can be used to write game bots or mouse/keyb simulations.

The CodeTime platform covers every aspect of parallel software from authoring, through distribution, to run-time. Its goals are: high programmer productivity; write once, run high performance anywhere; and wide acceptance.

CodeWhisk is an input method for Android that is designed to make programming code entry efficient (and fun!)

CoffeeTables is a high-performance, large-scale scientific data storage and retrieval Java library. CoffeeTables supports multiple storage backends, including CSV and HDF5.

Collaborative Filtering in Dating Services

This software allows analysis based on queuing theory. The software is simple and intuitive.

CollOPort provides a web-based portal for a group of researchers to use to collaboratively manage an observatory or experiment. It consists of several components, including topic-based collaborative content, discussions, proposals, and voting.

Collaborative Computational Science is an open source framework to encourage collaborative experimentation in computational science.

The collaborative framework Conzilla has primarily been developed to enhance the concept browser Conzilla (http://www.conzilla.org) with collaboration facilities. The Collaborilla framework is generic and can be used by other projects as well.