Open Source Java Scientific/Engineering Software - Page 55

The increasing wealth of transcriptomic data and current computational tools enable to infer how protein interactomes and complexomes may be assembled in specific samples. With CompleXChange this information can be exploited to conduct differential analyses of the dynamic protein complexome in a quantitative manner. The corresponding publication can be found on https://doi.org/10.1186/s12859-019-2852-z.

Java program for computations with values expressed in terms of physical or other units. Supports complicated mathematical expressions and user-defined functions. Invoked from scripts, line command, or as GUI. Extensive units data base.

Convert user-saved tracks from GPS-Tracks for iPhone to KML files for Google Earth. The GPS-Tracks iPhone application is available from the App Store or from http://www.gps-tracks.com . It can save recorded GPS tracks to the iPhone storage. This little Java applet provides the functionality to convert these saved tracks to KML files, for use with Google earth. Under Windows, it uses the synced files from the iTunes phone files backup, and extracts the tracks from there. Under Linux, it uses the virtual file system provided by libgpod (which provides an iPhone-gvfs-bridge) and gvfs-fuse (which offers gvfs virtual filesystems as Linux FUSE filesystems). Please note that this app is rather rudimentary. If you run into problems, please open a ticket to describe the issue; time permitting, I'll try to fix it.

CopperCore, a J2EE runtime engine for IMS Learning Design which can be used to incorporate IMS Learning Design in your own application(s).

This program accompanies the paper "Counting large distances in convex polygons" by Filip Moric and David Pritchard. The program, written in Java, searches a finite set of distance configurations in order to deduce theorems about convex polygons.

This software is used to create and modify machine programs for EMCO Compact 5 and Control T.U. CNC-2A lathes and to send / received them between PC and machine over serial connection and ethernet using a converter (like lantronix XPort).

CryptoHelper is a Java program designed to aid in the decryption of classical ciphers, ie pre WWII ciphers. It brings together tools like frequency analysis, friedman tests, enciphering/deciphering for several clasical ciphers, and brute force algorithm

Crystalsim is a simple freeware program with a neat graphical user interface for X-ray diffraction (XRD) data analysis . It can simulates all possible {hkl} planes data for the selected crystal. Crystallographic Information File (.cif) can also be used. Analyze both powder diffraction and single crystal data . Indexed at International Union of Crystallography (IUCR). Crystalline lattice parameters such as ‘a’, ‘b’, ‘c’ as well as interfacial angles such as alpha, beta, gamma can also be entered manually. Processed data can be saved as .csv file format. Designed by M Kanagasabapathy, Associate Professor, Department of Chemistry, Rajus' College, Affiliated to Madurai Kamaraj University Rajapalayam (TN) India email: rrcmks(at)gmail.com

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.

A lightweight and scalable genome browser

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.

The DERI Ontology Management Environment (DOME) is developed by the Ontology Management Working Group (OMWG). The aim is to provide tooling support for Editing & Browsing, Versioning & Evolution as well as Mapping & Merging.

DORY is a java program developed for searching KASH protein in large protein databases (in FASTA format). DORY is upgraded to DORY2. DORY2 required BLAST+ to run. ***Please make sure BLAST+ is installed on your computer.*** Please see the following publication for detail: Zhou X, Graumann K, Wirthmueller L, Jones JDG, Meier I (2014) Identification of unique SUN-interacting nuclear envelope proteins with diverse functions in plants. The Journal of Cell Biology 205(5):677-692. http://jcb.rupress.org/content/205/5/677.full Please see other useful tools for biology research: https://sourceforge.net/projects/cloversystem/?source=directory

DarSens is about distributed activity recognition based on acceleration data.

Darcy is a software for distance cartogram creation based on Waldo Tobler bidimensional regression.

Darwin 2: Java Framework for Evolutionary Computation (genetic algorithm, GA). A true framework with out-of-the-box functionality and extensibility of all classes. Interface-based pattern with dependency-injection to configure components.

Impressum / Legal Notice Sven Mostböck Murlingengasse 25/5 1120 Wien Austria e-mail: sven_mostboeck@users.sourceforge.net second contact option: use the open discussion on the FCSalyzer sourceforge page: http://sourceforge.net/p/fcsalyzer/discussion/ Information: Flow cytometry software is a perfect way to analyse complex data sets with large sample size. Data can be easily visualized to identify correlations and subpopulations. Subpopulations can be selected and analysed separately. However, such software required data in the FCS data standard. Data2FCS converts data from text files to FCS data files. A special treat is the possibility to transform categorical data into numerical data. The resulting FCS data file can be analysed in regular flow cytometry softwares, such as the open source FCSaylzer. For more info, take a look at the Wiki. Data2FCS needs Java 1.7 or higher to run.

DataFarming - A suite of software to support data farming of models

Applications to support the efficient capture of data from natural science collections specimens (particularly entomological collections), by facilitating pre-capture of data reflecting the storage structure of the collection, imaging of the specimens to separate data capture from specimen handling, and community sourcing transcription of hand written label data. Designed and written by a team at the Museum of Comparative Zoology. Includes a PreCapture barcode application refactored from this code base with support from the US National Science Foundation ADBC TCN for New England Vascular Plants NSF #1208835 Precapture Application: http://doi.org/10.5281/zenodo.154176 Migrated to GitHub PreCaptureApp: https://github.com/MCZbase/PreCapture Desktop App https://github.com/MCZbase/DataShot_DesktopApp Web App components: https://github.com/MCZbase/datashot_ejb https://github.com/MCZbase/datashot_web https://github.com/MCZbase/datashot_ee

Database Driven RoboCup Rescue Server is a version of RoboCup Rescue Server (https://sourceforge.net/projects/roborescue/) which uses a database to store the simulation data in order to simulate a very large number of agents.

This project is an extension to Jadex Framework and aims to develop an autonomous agent which is using adaptive decision making architecture based on Thagard’s deliberative coherence.

DevLogger is a software framework used to collect, monitor, and log data from any number of instruments or input devices simultaneously. Initial support provides for serial connections to Radio Shack 22-812 multimeters and My Weigh HD Scales.

Dicodess is a software framework for developing distributed cooperative decision support systems. It helps build DSS for mission-critical decision-making situations happening in dynamic, rapidly changing and often unpredictable distributed environments.