Skip to end of metadata
Go to start of metadata

The SyBIT Tech Days are the SyBIT project meetings where we keep each other up to date about our work, discuss about current topics inside SyBIT. Project partners are most welcome to attend as well.

Register here, previous registration link (do not use now)
please enter your menu choice

University Bern, 9.30 - 16.30

Location University of Bern, Main Building, Room 331
How to get there: Use main building left side entrance, climb to the 3rd floor. The meeting room is on the right.

Agenda: openBIS, KNIME and iBRAIN2






Peter Kunszt


Part 1: openBIS integration patterns



openBIS Integration Patterns - What is it?

Bernd Rinn


Integration Pattern: Configuration only
Show how openBIS can be integrated into a lab by using features that are part of the openBIS core distribution and configuring them appropriately.

Manuel Kohler


Integration Pattern: Data Store Server plugins
An introduction to writing simple but useful plugins for the openBIS Data Store Server to provide a level of integration that cannot be achieved by configuration alone. We will show an example of how to make openBIS fit data produced in your lab by writing a simple ITypeExtractor and IDataSetInfoExtractor. Provide a customized data set report by implementing your own IReportingPluginTask.

Chandrasekhar Ramakrishnan


Coffee Break



Integration Pattern: Custom relational data model
Demonstrate how to let openBIS manage a custom relational model, how to let the Data Store Server automatically populate this data model as new data sets are uploaded to the system and how you can manage named, parameterized SQL queries in openBIS that all users of the system can run with any parameters they like.

Franz-Josef Elmer


openBIS public remote APIs: Design Principles
We explain the design principles behind an openBIS public remote API and how this will benefit developers using them as well as system administrators and users who maintain and use pipelines that are built upon them.

Bernd Rinn





Part 2: openBIS public remote APIs



Quick intro: The Screening API
This slot will show how to use the openBIS public remote API for Screening to integrate openBIS with your application or workflow.

Tomasz Pylak


Hands-on session: use the API yourself
Java programmers who have a Java Development Kit or IDE (e.g. Eclipse) on their machine can start getting experience on using the openBIS public remote Screening API (an API recently added to support High Content Screening results), starting from a simple demo program.

Java programmers


Part 3: Workflows



Intro to Workflows
We present an overview of workflows used in, in the proteomics, genomics and screening communities. We then focus on a long-term vision of how to create and manage new workflows.

Ela Hunt


Intro to iBRAIN2

Michael Podvinec


iBRAIN2: Architecture

Eva Pujadas


iBRAIN2: Workflows

Vincent Rouilly


Coffee Break



Part 4: Discussion



Open discussion on challenges in the construction of workflows
Workflows are an important aspect of many data analysis projects within SystemsX. During this session, we want to present and discuss different aspects and open questions related to workflow processing, such as:

  • Existing constraints and requirements for scientific workflows in SystemsX
  • The workflow engine ecosystem. What is out there, and what needs to be supported? (Matlab, Python, C++, KNIME, Perl, Ruby...)
  • Standardization efforts to support workflow/module interoperability (data models, data access)
  • Tools required to support scientific workflows

presented by Eva and Vincent,
moderated by Michael Podvinec



Peter Kunszt

  File Modified
Microsoft Powerpoint Presentation Bern28thApril2010.pptx Apr 28, 2010 by
PDF File Sybit_tech_day_28_April.pdf Apr 29, 2010 by Kohler Manuel
PDF File Sybit_2010_TechDay_BBCF.pdf Apr 29, 2010 by Jacques Rougemont
PDF File SyBIT_TechDay_DSS_Hello_World_w_Notes.pdf OpenBIS Integration Patterns: DSS Plugins Apr 29, 2010 by Chandrasekhar Ramakrishnan
PDF File iBrain2_presentation_short.pdf Apr 29, 2010 by Michael Podvinec
PDF File 100428_sybit_techday_ibrain2.pdf iBRAIN2 current architecture Apr 29, 2010 by Eva Pujadas
PDF File SyBIT_TechDay_integration_patterns_intro_2010428.pdf Intro into the openBIS integration patterns session Apr 29, 2010 by Rinn Bernd (ID SIS)
PDF File SyBIT_TechDay_openBIS_public-APIs-20100428.pdf openBIS Remote Public APIs: Design Principles Apr 29, 2010 by Rinn Bernd (ID SIS)
ZIP Archive DSS Hello World Eclipse Project Aug 12, 2010 by Chandrasekhar Ramakrishnan
  • No labels