Meeting with the SIB Education Board

Ela and I also had a meeting with members of the SIB education board, Marc Robinson-Rechavi, Patricia Palagi and Frederique Lisacek. They have shown us what the SIB has organized until now. They have several pages where the education activities in Bioinformatics in all of Switzerland are easily accessible:

There are basically three levels of courses: the regular Masters classes (per semester), PhD courses (semester or summerschools) and courses for further education which can be just a couple of days or a week.

The agreement was that for Bioinformatics we (SyBIT and in general) simply attach ourselves to these pages, ie. if we plan courses we will advertise them here or if someone asks for courses we direct them there as well. We are going to actively suggest to our partners to do the same.

We will keep close contact to exchange information about education needs, and I offered our help to disseminate information about these pages in Zurich and Basel, or also prepare and create courses should some need arise that we could address.

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SyBIT Presentation, Lausanne

Today I had a presentation in Lausanne for Sebastian Maerkl’s group (DynamiX project). It was the same kind of presentation as in Bern earlier the same week, describing what SyBIT is about and what we are doing. Jacques Rougemont was also there and most of his group, as well as Ela.

Sebastian gave us a tour of his lab after the talk and explained how their data acquisition and analysis works. They have a very similar data management challenge as the screening community, producing large numbers of images and videos that need to be analyzed using image analysis methods. They have their own cluster in the laboratory for the analysis. We will look at possibilities to help them with the metadata management in a followup meeting next week.

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I attended those two conferences in Lausanne, 22-26 March 2010. ICDT is a database theory conference while EDBT focuses on practical database topics, with less theory and more papers involving the benchmarking of new algorithms and solutions which at some later stage get incorporated into software products. The conference featured keynotes, regular papers and demos, and several workshops. The most interesting keynotes in my opinion were by Ian Horrocks on scalable semantic systems – those systems are not currently scalable at all, and by Pierre Fraigniaud on the importance of succinct labeling in XML data storage in databases. The demo session featured a B-Fabric demo by Fuat Akal et al., B-Fabric: The Swiss Army Knife for Life Sciences. This was a very comprehensive presentation of the rich set of databases supporting biological data analysis at the FGCZ in Zurich. I also attended some talks on the efficient querying of workflows, data provenance and data integration. New trends in databases include also the use of new architectures. I found a tutorial by the ETH Systems group to be of particular interest – on the use of FPGAs in databases, and a paper on the use of multicores in suffix tree construction. The PhD workshop had an interesting talk on web page archiving (by French Television/Radio) and also a talk on research funding by Moira Norrie of the ETH. Via informal discussions I also learned about some interesting databases and tools which could be used for prototyping in work, in particular I liked the BaseX from Konstanz.

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SWITCH Storage WG in Bern

Today i attended the SWITCH Storage Working Group meeting. It was very well attended, many of our SyBIT partners were present (FMI, Biozentrum, UZH, ETHZ, EPFL) and also infrastructure people from other universities and universities of applied sciences. In the morning some sites have shown what they have in terms of storage and how they do things. Except for our partners most have focussed on storage infrastructure for the ‘commodity’ services like administration (SAP db, finance files), email, user’s home directories, backup. We have certainly the largest amount of scientific research data, and it easily surpasses all of the other kinds of data. But in terms of technology being used there was a lot of overlap, and it was suggested by several people to cooperate when acquiring hardware and software and to exchange information.

There were presentations on cloud storage, on ideas for distributed archiving and by SWITCH on network pricing. Cloud storage in terms of private cloud storage was seen as useful, but using commercial providers for long-term storage is obviously too expensive. The technology however is interesting also to share data and resources among universities, especially since with SWITCH we would not have any network costs. Small universities could profit from bigger ones, and the big ones might also exchange resources among each other.

The distributed archiving idea is about duplicating data (read only archive data) accross several sites for safety. Each site can have its own long-term archive solution, but for certain data that needs more security and several off-site copies, this is a proposed mechanism to achieve it (storage broker presentation). For the copy mechanism they suggested bittorrent..

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SyBIT Presentation in Bern

Today I had a presentation in Bern, at Chris Kuhlemeier’s lab. (We have a SyBIT project together with Richard Smith, working on a confocal imaging software that he has written. SyBIT pays Thierry Schuepbach (from VitalIT) to do some consulting and coding.) There were around 10 people in the audience including Chris, so it was quite an informal setting with many questions and discussions.

I have explained what SyBIT is and what we intend to do and have shown them our projects so far. They were very interested on all levels, including local file management and tracking for which they might be interested in an openBIS instance, basic lab document handling (a wiki) and also bioinformatics consultancy in genetics.

The consultancy or help they need would also be for the research they do on the tef plant, see the last X-Letter, page 6pp on the topic concerning bioinformatics help. I had a nice tour with Dr. Tadele visiting his plants and lab.

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CloudSuisse Conference

Today I attended the first CloudSuisse Conference. Almost all of the talks were in German (except the one from Amazon) but the representation was quite international. In the morning the ‘big’ players have shown what they currently have to offer (Amazon, Google, Salesforce, Microsoft, Cordys) and in the afternoon there were several tracks where local companies have shown what they do. This was a purely industrial event, but also some non-industrial people were present, like from the Swiss topographical institute (the guys with the Swiss maps) who use Amazon to provide a high-end map service to their users.

You can read more about CloudSuisse at their official website.

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On Finance and 2nd Party Funding

The finance reporting is now over, but there have been many uncertainties about 2nd and 3rd party funding and how they should be reported (or not). 2nd party is defined as relevant funding in the same scope coming from other public and private funding agencies (EU, SNF, etc). 3rd party funding is funding through industrial collaborations. See the Finance Handbook for the exact definition. needs to report (to political bodies mainly) how much additional funding and collaboration was “generated” by Obviously this is very hard to assess, and there are no clear instructions and rules. If you have perfect overlap between say an EU project deliverable and a deliverable and claim this on both sides, you would have received double funding, and both the EU and would claim their money back. However if you can only do certain work because of the perfect overlap, ie. do work that otherwise would not have been possible and the funding is complementary, then you do exactly what everyone wants to see. But again, this may be a fine line to walk. If you can clearly specify synergetic effects, you should report them. There may of course also be only partial funding claimed for ‘synergetic effects that would otherwise not have been possible’, this is in your best judgement to specify.

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Discussion about the ETHZ D-BIOL IT Strategy

Today I have met with Jacques Laville and Nico Graf who are in charge of setting up and implementing a department-wide IT Strategy for the Biology Department of the ETHZ. They have written a long document explaining the reqiurements and major points of the Strategy. is explicitly mentioned as a partner, defining interfaces to their processes in the document. They foresee to integrate IT supporters at the individual institutes of the Deparment. These supporters would take care of the mundane IT support at hand (laptops, printers, etc) but also act as the interface to the InformatikDienste for larger projects (servers, storage, clusters). They also assure that information on new requirements and needs is properly communicated and that economies of scale can be exploited. All in all it is the same strategy as SyBIT but in a different context, and I mentioned to them that this is very nicely aligned with what we would like to do.

In the IMSB there is a new person that will take up this position as of this month. From now on we can directly communicate with him if we need any new infrastructure, this is a great help.

I also need to nominate our local SyBIT people to participate in some discussions as invited guests whenever topics are on the table that are relevant to Since we have Emanuel and Adam on site, I gave their names to Jacques. They will work together with the new person whenever we need IT services. Some existing tasks can be passed on to this person soon – after an accomodation phase of course.

We also agreed to organise two workshops – one about openBIS and its usage in D-BIOL (we have three instances by now) and they would like to invite someone from the OMERO community and an industrial partner to see what they have to offer. The first workshop will be organized by us.

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Discussion with Nicola Zamboni

Today I had a short chat with Nicola Zamboni, who leads our efforts for the YeastX metabolomics project. He is using the openBIS installation there quite extensively and has introduced is as a tool for all of the Sauer Lab. The amount of data being ingested is growing now, and he needs mechanisms to partition it, as also the actual metabolomics data is ingested into the DB, not just the metadata. It should be easy to partition the DB however into time chunks, ie. keep the total size almost constant and load only the most recent data, keeping older datasets stored on HSM storage (DB export). Whenever old data is needed, it can be reimported into the DB. CISD will work with him on this. He also says that now there would be a good time to add a UI to the system, right now he uses openBIS only as a back-end, integrating his own tools through the DB interface directly. The openBIS Web UI has not been used yet, and at any rate would need to be customized. That is a specific new project which we need to schedule but this will certainly happen.

Nicola made a very satisfied impression and seems very happy to work with us.

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