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****1/2 JabRef bibliography manager
JabRef is a graphical application for managing bibliographical databases. The main focus is on BibTeX databases, but other database formats will be supported as well. JabRef is distributed under the terms of the Gnu General Public License, runs on all platforms and requires java 1.4.
****1/2 Saros
Saros is a research project to enable distributed pair programming (also called remote pair programming) in the Java IDE Eclipse. Saros supports real-time collaboration by two and more peers and adds many features to increase awareness and presence regarding the whereabouts of each peer.
****1/2 ImageJ
ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.1 or later virtual machine. Downloadable distributions are available for Windows, Mac OS, Mac OS X and Linux. It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations.
**** Python and Scientific Computation
The home page for Scientific Computing with Python.
**** g3data
g3data is used for extracting data from graphs. In publications graphs often are included, but the actual data is missing. g3data makes the extracting process much easier.
**** Webolab
A web-based platform for collaborative research and high-performance computing interface, a tool for implementation of virtual labs. Supports Condor cluster management engine.
**** MathML in Mozilla
Project to add Math Markup language to our last best hope at an open source browser.
**** Open Visualization Data Explorer
IBM's famous volume renderer that does much much more.
**** Refbase, a web-based reference manager for individuals and groups
Refbase (based on PHP and MySQL) allows single users, working groups and institutions to share a reference database. It offers (amongst many others): - import and export functionality for for the most important formats (e.g. BibTeX, RIS, ...) - software independent "in-text-citation" (e.g. Latex, Word, OpenOffice, text-editors) - RSS features (e.g. all queries) - personal and institutional online publication lists - clean and standardized interface (accessible via web-browser) - user specific fields for personal keywords, notes etc. - available in several official Linux repositories (Gentoo, Madriva) - good documentation and support ;-)
**** LabPlot
Data analysis and visualisation. A new KDE-based graphing / plotting package that looks very powerful.
**** Fityk
Fityk is nonlinear curve-fitting and data analysis software.
**** Grace / XMgr
Very versatile and powerful 2-d plotting package
**** cb2bib - From clipboard to BibTeX: A tool for extracting bibliographic references
From clipboard to BibTeX: A tool for rapidly extracting unformatted bibliographic references from email alerts, journal web pages, and PDF files. The cb2Bib facilitates the capture of single references from unformatted and non standard sources. Output references are written in BibTeX. Article files can be easily linked and renamed by dragging it onto the cb2Bib window. Additionally, it permits editing and browsing BibTeX files, searching references and the contents of linked files, and cite them into document editors.
**** PrestoPlot
A 2D plotting tool for Win32 Platforms (Windows NT/95/98/00) inspired by Grace/xmgr.
**** ScientificPython
ScientificPython is a collection of Python modules that are useful for scientific computing.
***1/2 BioCatalogue - the Life Sciences Web Service Registry
The BioCatalogue is a registry of biological Web Services. The BioCatalogue website is freely accessible to the world as it is searchable and indexable to search engines. It provides an open platform for biological Web Services registration, annotation and monitoring.
***1/2 Science Laboratory Inventory
Science Laboratory Inventory Control Management System and Orders: Web-based system that is useful for managing chemical and equipment inventory management and handling science labs orders from teachers to technicians for their practical sessions.
***1/2 Taverna Workbench and Server
Taverna is an open source domain independent Workflow Management System a suite of tools used to design and execute scientific workflows. Taverna has been created by the myGrid project and funded through the OMII-UK. Taverna has a guaranteed funding till 2014. The Taverna suite is written in Java and includes the Taverna Engine (used for enacting workflows) that powers both the Taverna Workbench (the desktop client application) and the Taverna Server (which allows remote execution of workflows). Taverna is also available as a Command Line Tool that for a quick execution of workflows from a terminal without the overheads of the GUI. Taverna allows for the automation of experimental methods through the use of a number of different (local or remote) services from a very diverse set of domains biology, chemistry and medicine to music, meteorology and social sciences. Effectively, Taverna allows a scientist with limited computing background and limited technical resources and support to construct highly complex analyses over public and private data and computational resources, all from a standard PC, UNIX box or Apple computer.
***1/2 Icy
Icy is an image analysis software primarily targeted at biological needs. It provides high-quality tools for biological image processing tasks, such as filtering (linear, nonlinear, morphological, etc.), cell segmentation, particles detection, tracking, multiple-class thresholding, measurements, microscope control, etc. It is designed to work on sequences from 2D to 5D (X, Y, Z, time, color channel), and runs on Windows, MacOS, Linux.
***1/2 myExperiment
The myExperiment Virtual Research Environment enables you and your colleagues to share digital items associated with your research in particular it enables you to share and execute scientific workflows. You can use www.myexperiment.org to find publicly shared workflows. If you want further access, and the ability to upload and share workflows, you will need to sign up.
***1/2 Veusz
A publication-quality scientific plotting package built in Python, NumPy, and PyQt4.
***1/2 OGSA-DAI
OGSA-DAI is an open source framework for executing complex data management scenarios (including data access, update, transformation, integration and delivery) involving distributed databases. It supports relational, XML and file resources. The supported functionality, data resources and presentation layers can all be customised or replaced. OGSA-DAI has been used to build applications in astronomy, medicine, geo-location, social sciences, environment, and transportation amongst others. OGSA-DAI, managed by EPCC, The University of Edinburgh, is 100% Java and is freely available under an Apache 2.0 licence from SourceForge (http://sourceforge.net/projects/ogsa-dai)
***1/2 RefDB homepage
RefDB is a reference database and bibliography tool for DocBook SGML/XML documents. It allows users to share databases over a network. It is lightweight and portable to basically all platforms with a decent C compiler. And it's released under the GNU Gen
***1/2 KMatPlot
KMatplot is a gnuplot-like tool for plotting data sets in either two or three dimensions. It can plot many types of 2d plots, including pixmaps and contours, and 3d surfaces. It offers a full WYSIWYG mode with multiple objects on a single page. As opposite to Gnuplot, KMatplot is very clickable, so easier to use for unexperienced users. It can be used instead of Gnuplot with Octave and Scilab - there are new dll functions installed in those packages, which communicate with KMatplot through an Unix socket. Those functions are named 'kplot', 'kimage', kmesh', ... and are similar to those found in Octave by default.
***1/2 Quickplot
Quickplot is a fast interactive 2D plotter with infinite zooming, value picking, pipe input, and unlimited plots displayed. Quickplot is meant for looking at your data quickly and of secondary importance is making static pictures of your data. It's a data viewer, not a plot editor. It reads ASCII text and sound files. It has lots of command line options, making it very shell script friendly.
** NCO
Tools for manipulating netCDF data files
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