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SyBIT is being run as a series of projects.

There are continuous projects and limited duration projects. New projects are always of limited duration. Any SystemsX.ch member can suggest a new project to SyBIT and receive resources from SyBIT to carry it out.

Please see the Project Application page.

 

Definitions

Active Continuous Projects and Support Tasks

All of the below also have associated Support Tasks since they have one or several actively used instances that need user support. That is in the nature of continuous projects.

 

Project Title

Type

Context

Project Lead

Team

Starting date

Wiki

Status

openBIS data management framework development and support

Regular

Large data volumes (almost all RTDs)

Bernd Rinn

CISD

2007

Project Wiki

Project Backlog

iBRAIN2 automated screening development and support

Regular

High Content&Throughput Screening projects

Michael Podvinec, Peter Kunszt

Eva Pujadas, Vincent Rouilly, Mario Emmenlauer, Ela Hunt

Oct.09

Project Wiki

Project Backlog

Proteomics Portal development and support

Regular

PhosphoNetX, Aebersold Lab

Lars Malmstroem, Peter Kunszt

Lucia Espona, Andreas Quandt, Zoltan Farkas, Akos Balasko, Gabor Herrmann

Aug.09

Project Wiki

JIRA

e-Notebook Wiki

Small

Any SystemsX.ch lab

Adam Srebniak

n/a

Jan.10

Project Wiki

In production

BioDB Database synchronization

Small

Any SystemsX.ch lab

Adam Srebniak

n/a

Oct.09

Project Wiki

In production

CycliX database

classical

CycliX

Nicolas Guex

Nicolas Guex, Robin Liechti, Dimitry Kuznetsov

Jan-09

Website

ongoing

LipidX database

classical

LipidX

Howard Riezman

Fabrice David

Jan-09

wiki, website

In production, major upgrade scheduled 2011

DSU workflow server

Regular / Support

Establish and support a Galaxy-based workflow server for working with DSU data

Bernd Rinn

CISD

2010-10-01

 

initiated

HTSStation analysis pipelines

classical

CycliX, DynamiX

Jacques Rougemont

Jacques Rougemont, Marion Leleu, Fred Ross, Yohan Jarosz, Lucas Sinclair, Fabrice David

Jan-10

Website

ongoing

Interface between iBrain2 and B-Fabric

Regular

 

Peter Kunszt, Lucas Marti

Aleksander Markovic, Can Türker, Lucas Marti, Marco Schmidt, Michael Podvinec, Peter Kunszt, Vincent Rouilly

Dec. 2011

 

finished

 

Active Limited Duration Projects

 

Project Title

Type

Context

Science Lead

Project Lead

Team

Starting date

Wiki

Status

LMC HCS Automation and Data Management

Regular

ETHZ-LMC (InfectX)

Gabor Csucs

Peter Kunszt, Ela Hunt

iBrain2 and openBIS, Emanuel Schmid, Karol Kozak, Csaba Balazs, Peter Horvath

Jan.10

Project Wiki Kickoff

HCS openBIS

Dehio HCS Automation and Data Management

Regular

Dehio Lab UniBAS (InfectX)

Christoph Dehio, Matthias Truttmann

Michael Podvinec

iBrain2 and openBIS

Apr.10

Project Wiki

in progress

Pelkmans HCS Automation and Data Management

Regular

Pelkmans Lab ETHZ (InfectX, LipidX, PhosphoNetX)

Pauli Rämö, Lucas Pelkmans

Ela Hunt

iBrain2 and openBIS, Emanuel Schmid

June 10

Project Wiki

starting

OMEGA

Regular

Microscopy, AIDS infection tracking (UniGE)

Jeremy Luban

Caterina Strambio, Ela Hunt

Vanni Galli, Raffaello Giulietti, Mario Valle, ..

Oct.10

Project Wiki

started

Image viewing with interactive features for screens in openBIS

small

openBIS for HCS

Karol Kozak

Bernd Rinn

Adam Srebniak, CISD

Oct.10

 

in progress

openBIS installation for DynamiX

classical

DynamiX

Sebastian Maerkl

Bernd Rinn

CISD, Dmitry Kusnetsov

Aug.10

 

instance installed, importing mechanism in place

Data Integration

classical

DynamiX

Sebastian Maerkl

Jacques Rougemont

Nicolas Denervaud, BBCF

2009

Project Wiki

ongoing

openBIS integration with Cell Profiler

classical

LipidX

Jean Gruenberg, Cameron Scott

Nicolas Guex

Dimitry, Olivier, Arnaud

2008

 

In production since 2008, several runs analyzed and processed

MS pipeline

classical

LipidX

Nicolas Guex

Fabrice David

Fabrice David, Nicolas Guex

Mar-09

 

ongoing

ChIP-seq analysis pipeline

classical

CycliX

Jacques Rougemont

Jacques Rougemont, Nicolas Guex

Eugenia Migliavacca, Olivier Martin, Dmitry Kuznetsov, Yohan Jarosz, Fred Ross

Sep-10

 

ongoing

Interactive genome browser

classical

CycliX, DynamiX

Jacques Rougemont

Jacques Rougemont, Marion Leleu

Yohan Jarosz, Lucas Sinclair, Fabrice David, Bernhard Sonderegger

Jan-10

wiki, website

ongoing

WingX primer design workflow

Regular

WingX ETHZ

Ben Schlager

Ela Hunt

Emanuel Schmid

May-11

WingX Primers

starting

 

Projects in Planning

 

Project Title

Type

Context

Lead

Starting date

Comment

Reservation System concepts

small

SytemsX.ch labs

Thibaut Siegmann

?

Easy to use intuitive online instrument reservation system

Fly Food management

small

WingX

Julie Lüdke

Oct.10?

checking possibilities

CellClassifier

Regular

iBrain2, HCS

Mario Emmenlauer

Nov.10?

Classification of cells automatically in images - automation as much as possible..

DeepSeq Pipeline

Regular

Deep Sequencing

Michael Stadler, Christian Beisel

Dec.10

The deep sequencing analysis pipeline by Michael Stadler needs to be redone from scratch and integrated into the DSU units workflows

 

Completed Projects

 

 

Project Title

Context

Science Lead

SyBIT Lead

Starting date

Link

Results

GridCertLib

Security, Portal submission, SWITCH-AAI

Peter Kunszt

Peter Kunszt

Jun.10

Project Wiki

library done and available, publication submitted

CRK Webfrontend

Structural Biology tool for SystemsX.ch, PSI

Guido Capitani, PSI

Adam Srebniak

Feb.11

Project Wiki

Tool is done and operational. Infrastructure is being set up at PSI.

MorphoGraphX Imaging Tool

Plant Growth small, Confocal Imaging

Richard Smith

I.Xenarios

Feb.10

SVN

Working client-side tool for visualization of confocal data in 3D

Software Repository of IMSB

PhosphoNetX

Lars Malmström

Adam Srebniak

Feb.10

Project Wiki

Repository has been setup

Proteomics Data Upload

PhosphoNetX

Lars Malmstroem

Bernd Rinn, Emanuel Schmid

Mar.09

 

All data now in openBIS.

Improvement of deep sequencing sample tracking

Cell Plasticity

Christian Beisel

Bernd Rinn, Manuel Kohler

Oct.09

 

The DSU unit is now using the openBIS instance in production, Publication

BioFormats c++ extensions

Imaging Community

Patrick Schwarb

Mario Emmenlauer, Peter Kunszt

Oct.09

See the Project Wiki. Get the lib here

The library has been 0 and deployed.

New Web pages

small

Peter Kunszt

Dean Flanders, Thibaut Siegmann, Ela Hunt

Jun.10

http://www.sybit.net

up and running. content needs continuous management

Content Management Systems (for RTDs and communities)

small

SystemsX.ch Community

Dean Flanders

Oct.09

 

Webvanta service up and running, several websited deployed, adding new ones is easy

YeastX MS Data Integration

YeastX

Nicola Zamboni

Bernd Rinn

Apr.09

 

The initial project delivered the database for integrating the MS Data. A followup project has been defined.

YeastX Data Integration Consolidation

YeastX

Nicola Zamboni

Bernd Rinn

Sept.09

Project Wiki

Upgrade is complete, new system is much more performant and faster.

LiverX Result Curation

LiverX

Niklaus Fankhauser

Bernd Rinn

Apr.09

 

The schema has been defined and delivered, now integration is being done in the RTD

LipidX Imaging

LiverX

Nicolas Guex

Nicolas Guex

Jan.09

 

An openBIS instance was set up to manage the data and is in use now

E-Notebook

Community

Ernst Hafen, Fritjof Helmchen

Peter Kunszt

Oct.09

 

The initial project's aim was to estimate feasibility. The followup project will implement a concrete first wiki+openBIS notebook solution.

Software Repositories

SyBIT, PhosphoNetX

Lars Malmström

Adam Srebniak

Oct.09

Project Wiki

The repository is built and available. Now it needs to be filled with content.

Community Meeting Organization

SyBIT

Peter Kunszt

Ela Hunt

Oct.09

 

Community meetings have been held. Communities have started to organize themselves.

Interface between iBrain2 and B-FabricBattleXLucas MartiPeter KunsztDez.11 bFabric and openBIS interface has not been completed but Lucas Marti has left. This project was NOT successful.