PI Meeting Bern

There was a meeting of all RTD PIs in Bern yesterday morning. I have given a presentation on SyBIT.

First, i’ve gotten some additional names for the communities that i’ve listed, mostly from CINA and Neurochoice.

Then there was a long discussion initiated by Ernst Hafen from WingX concerning an electronic lab journal. He said that now this is again a very hot topic due to the recent resignation of the ETH Vice President for research. He said that it would be something that at least he would be interested in developing together with SyBIT. Neurochoice (Fritjof Helmchen) also said that they would participate. The other people said that basically they would be very interested in something that works, because they all had some previous attempts to introduce something that failed, either because it was too expensive or because it did not meet their needs. I asked what they used today or how they would like to work, and as far as i can tell a wiki system combined with a database backend would already go a long way. It was agreed that we at least would pick up this discussion with WingX and Neurochoice and see what we can do on a reasonable timeframe. It was agreed that it should not be a big thing but something focussed that solves the most basic need.

Finally there was also a long discussion on how to go about publishing data. I have presented the slide that all data should be ‘public after 2 years’ and explained to them that basically this means that they now have the opportunity to think about a policy how they would like to do this now or someone else will think about a policy for them in a couple of years time, and then it will not be such that they like it. Here people liked the community approach that each community would get the mandate to define the publication policy.

Posted in Updates. No Comments »

Presentations updated

All presentations that i’ve given so far on SyBIT are now in the Wiki. I’ll try to keep it up-to-date. If you have any, please just add it to this page.

Posted in Administrative. No Comments »

Discussion with IT D-BSSE

I had a discussion and lunch with Janos Palinkas, head of the IT services at the D-BSSE. We have informed each other about our current plans and needs. He seemed quite favorable of an infrastructure community. He stressed however that he is not an ‘enabled’ person, ie. he cannot make any decision without getting explicit approval from the Department Head. This includes any requests for hosting or collaboration. The current Professor, who has been in the position of Department Head only for a few months (this is a rotating appointment) is not yet up-to-speed with the needs and issues around the IT services. In addition, being an ETH Zürich entity, there are specific constraints on how the machine room has to be built and how the network has to be set up.

What SyBIT can help with here is voice the interest and need for cooperation with the BSSE IT team explicitly, with concrete proposals and plans to be executed (costs included of course). These then can travel the ‘official path’, top down in this case. Janos’s official boss is Jörg Stelling if i understood correctly.

Posted in Infrastructure. No Comments »

CellPlasticity – Deep Sequencing Platform Meeting

Two days ago we had a meeting in Basel about the needs of the CellPlasticity (former CPHD) project concerning the interaction with the Deep Sequencing Platform run by D-BSSE. All players have been at the meeting, both from the scientific side and the BSSE platform responsibles.

Currently the platform is being operated under the responsibility of Christian Beisel, who does this however not as his main job but ‘on the side’ next to his own research. There is one full-time wet-lab person assign to operate the machine and 50% IT support through Manuel Kohler at CISD. This used to be 1FTE until recently. One of the concerns expressed was that this level of support will probably not be sufficient or scale when the demand for the platform goes up in the future. This is where SyBIT will help on the immediate timescale.

Christian will come up with a set of requests within the next 2 weeks and a timeline. He will send us a detailed list of things to do, and will prepare it in tight interaction with the FMI an the Biozentrum.

Posted in Infrastructure. No Comments »

Visit to UCL

I have been to the University College of London visiting Arthur Thomas, who is member of the SyBIT Management Board and recently has been appointed to a position at UCL for “Computational and Systems Medicine”. He arranged for me to meet with several very knowledgeable people on computing and data management for biology.

First I’ve met with Kerstin Kleese Van Dam, Director of IT for the Faculty of Biomedical Sciences which is responsible for the support of over 8000 people. They support not only the basic biomedical research but also software development. We had a very interesting discussion with the following highlights:

  • She reinforced the idea to be as close to the scientists as possible while supporting them and thought the way SyBIT is doing it is the right way.
  • She also supports platforms around equipment and services, like a gene sequencing machine or a visualization platform. So SyBIT’s communities also go in the right direction
  • She stressed the importance of education to assure the new tools are adopted and used
  • Data publication and curation policies are necessary but they have to have ‘teeth’, ie. come from the funding agencies with real monetary consequences if someone ignores them otherwise everyone will ignore them
  • If you have good policies, there have to be centers that can take the data and manage them and help scientists curate them
  • Annotations have to come out of the labs already, automation can help and also electronic lab journals. Local IDs need to be publishable already.

Best Practice Tips:

  • Aim for permanent support embedded in the institutions, but avoid ‘staff capture’ through line management. A quality needs to be kept to build and keep trust.
  • Be involved in the science projects, help early in proposals bringing in the experience and network (we know someone else who has done this or that), this can save money and improve the proposal
  • Assure faculty knows the details and values the work done, engage them through trainings and education
  • A very successful concept was also the Personal Shopper service to buy equipment and save money


The I met with Jeremy Yates, deputy head of Research Computing (the HPC group) and Denis Timm, who runs the bioinformatics cluster in the Computer Science department. Although they look like coming from a different domain (physics and CS) they have supported the bio community for many years. The problems are very similar to the ones we have in individual institutes in CH, especially in the ETH to build the infrastructure for data management, and to educate people how to use it. We discussed the advantages and disadvantages of on-site storage, federated storage grids, data workflows etc. They also agreed that the best model to support people is the ‘tall thin man’ model where one person knows the whole data flow end-to-end and can support the community.

They would like to collaborate in the domain of application validation, i.e. if there is a code developed by someone, if they know that we support it and ‘validate’ it that it is working under such-and-such conditions, that they can simply take it up and use it. And vice versa. Similar to the numeric analysis community in physics. A community wiki to share information is also their preference.

Over lunch we met with Jacky Pallas, who coordinates Platform Technologies (omics, etc.). Also present was Elia Stupka. We have been discussing very similar points as with Kerstin Kleese Van Dam, she also confirmed that the setup of SyBIT is useful and said that if we can support the Swiss community this way, it would be a great example for the rest of the community. She also gave an insight into how funding works in the UK.

Finally, we met Buzz Baum, coordinator for systems biology, who has explained to us several projects he is involved in. He was already at the science-end of the ‘tall thin man’, expressing a strong interest in support for basic applications and tools.

Posted in Trip Reports. No Comments »

Coordination Team Meeting Bern

Today we had a coordination team meeting in Bern. We have agreed on the most important points how to work together in SyBIT, although it has become clear that there are tangible differences in local culture and the way people work. We have defined 6 technology-oriented communities:

  • High Throughput Screening
  • Genomics (Deep Seq, Mircoarray, Realtime-PCR, ..)
  • Proteomics (MS applied to proteins and their compounds)
  • Low-Level Data Management (Storage, Raw data, Provenance metadata)
  • Computational Biology (Tooling and automation of data analysis, bioinformatics, Information Systems, modeling)
  • Microscopy and Custom Instruments

We have also identified the people we would like to invite to participate in these communities. In addition, there will be also a purely computing infrastructure-oriented ‘community’, composed of the local infrastructure providers.

We have also discussed how new projects will be initiated in SyBIT. There are basically two ways:

  1. An RTD or several RTDs approach SyBIT with a project idea. These will be treated according to the RTD’s prioritization (showstopper – important – nice to have)
  2. A subset of a Community approaches SyBIT with a project idea. This will be prototyped and shown to the entire community and some interested RTDs. It will be prioritized according to the reactions – or dropped if people are not interested.

Next steps:

  • Information inside SyBIT coordination team will be distributed using a Blog written by PK. He will assure also the information flow inside the team.
  • The next meeting will be a phone / video conference in October
  • We will organize a parallel session during the All-SystemsX-Day in Novenber in Bern, to motivate people to participate in the various communities.
  • The Wiki structure will be reworked by FMI (DF, TS)
  • A project charter template will be provided by MP
  • An evaluation of current project management tools like sourceforge will be done by CISD.
Posted in Updates. No Comments »

Starting Blog

The purpose here is to keep everyone up-to-date what is happening in SyBIT. It’ll be written by me mostly and therefore be completely subjective. If you see i got somthing wrong, don’t hesitate to post a comment!

Posted in Administrative. No Comments »