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SyBIT Toolbox

Software in this category is actively supported by SyBIT and co-developed by SyBIT. Mostly SyBIT attaches itself to existing developments to improve tooling already being used based on a request by the SystemsX.ch scientists.

Name

Description

Supported By

openBIS

openBIS is an open source Biology Information System

CISD

CIFEX

The CISD File EXchanger allows internet users to exchange large files (up to 12 GB).

CISD

Datamover

The CISD datamover is a program that takes care of moving (typically large to huge) file-based data produced by a data producer (e.g. a measurement device) to a (remote) central storage.

CISD

Genome data viewer GDV

A java-based interactive genome browser web utility.

BBCF

Bein

A web based workflow manager and data store for exploratory data analysis

BBCF

XuvTools

XuvTools is a fully automated 3D stitching software for biomedical image data

FMI, LMC

iBRAIN

iBRAiN is an acronym for image-Based RNAi and was developed as a middle ware between image analysis software, content management of siRNA libraries, the storage of large sets of microscopy images, the distribution of computation jobs on large computer clusters, and the harvesting and visualization of obtained results.

IMSB, LMC

Software used by SystemsX.ch RTDs

This is a list of software used by SystemsX.ch RTDs.

Name

Description

Used By

ImageJ

 

many

Infomix

 

LipidX

TPP

 

PhosphoNetX

.

 

 

Other interesting tools and software

Name

Description

Project Site

Other useful links / information

Platform

Used By

Screen

Terminal Multiplexer

http://www.gnu.org/software/screen/

Manual
Wiki

Unix/Linux/MacOSX

Arnaud Fortier

iTerm

Terminal

http://iterm.sourceforge.net/

 

MacOSX

Arnaud Fortier

Hotspot Shield

Free VPN

http://hotspotshield.com/

 

PC Mac

Arnaud Fortier

Arpoh Sprintmate

Online SCRUM project management

http://www.arpoh.com/sprintmate/

Easy to use project management of scrum projects

Online (any)

Thibaut Siegmann

Quickcheck

Software testing

http://en.wikipedia.org/wiki/QuickCheck

There are versions for Java and Perl among other languages.

Many, see wikipedia

Fred Ross

Slims

Simple LIMS and instrument management

Doc

 

Online

In evaluation

Other Collaborative Tools