Archive for category conference report

The BioSysBio conference 2009

The Genomics GTL Pictorial Program.
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The premise of the BioSysBio conference is to

bring together the best young researchers working in Synthetic Biology, Systems Biology and Bioinformatics, providing a platform to hear and discuss the most recent and scientific advances and applications in these fascinating fields.

This years BioSysBio 09 has just taken place in Cambridge, UK. The program was more slanted towards synthetic biology rather than more traditional systems biology, which I think reflects the growing momentum that synthetic biology has gained in the past year. I think this is a good progress and  I was secretley glad as I did not want to spend 3 days looking at massive network diagrams squashed onto power point slides.

This was the first conference I had been to that the organisers actually requested that we use the BioSysBio FriendFeed room and Twitter to communicate, so I did. Half way through the first day the organisers demonstrated the FF room, which seemed to exist solely of Allyson’s posts, and questions were asked if she was a blogging bot. When we did confirm there was actually a female at an engineering conference, she was thereafter known as the BioSysBio poster girl.

As ever Ally was monumental in her blogging during the conference and all her posts can be found here. At one stage Simon did try to blog her talk to the same detail and speed, but he just kept coming up withe excuses about the wifi being slow – eventually he got there.

This was the first time I attended BioSysBio and I thoroughly enjoyed the experience. In general all of the talks were of a high standard most notable for me were Allyson Lister’s talk on Saint: a lightweight SBML annotation integration environment, Christina Smolke on  Programming RNA Devices to Control Cellular Information Processing, Piers Millet on Why Secure Synthetic Biology? and Drew Endy on Building a new Biology. It was also good to hear about improvements for the Registry of standard biological parts by Randy Rettberg and the wiki style community building of the product catalogue, or data sheet about each part.

There is no point in me re-posting coverage that has already been documented, so if you would like to follow what happened you can follow the #biosysbio twitter stream, the biosysbio FreindFeed Room, or if you want a more comprehensive overview, Ally’s blog.

This was also the first time I had used twitter (via tweetdeck) instead of Friendfeed to microblog a conference. This approach certainly generated alot of noise and random soundbites, and was probably a fast way to make notes. However, although everything is grouped under the #biosysbio tag, they are not grouped around a particular talk or discussion thread. I can’t help thinking that microblogging via FriendFeed would be more focused around a specific talk and provide a more focused discussion, as opposed to just covering what was happening second by second.

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The UK e-science All Hands Meeting 2008

Edinburgh, ...Image via Wikipedia

The UK e-science All Hands Meeting (AHM) 2008 is currently underway in Edinburgh. I will not be taking notes via this blog, instead I will be microblogging via my FriendFeed. Other delegates already on the FriendFeed band-wangon are Daniel Swan and Jean-Claude Bradly. Hopefully by the end we will have some more e-science FriendFeed converts. I will also be tagging AHM relevant posts via delicious using the tags e-science+AHM+ 2008.

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The First MIBBI workshop: Day 2

The second day of the MIBBI workshop was more “free flowing” compared to the first day. During the second day we focussed on the process of MIBBI, house-keeping, infrastructure and the website.

The main focus of the day was discussing what it means to be registered on the MIBBI site and be a member of the Foundry. As a straw man, rather than starting from scratch, we used the OBO foundry principles to see if they could be applied to reporting check-lists, and came up with a draft set of principles. A full “official” report of the workshop should be forthcoming.

As a break from the rigorous standards development and process of reporting check-lists we went to a local restaurant and experienced anarchy when it came to understanding the menu. The meal itself was brilliant, however some degree of semantic extraction had to be applied to the menu to actually understand what we were ordering – No fancy algorithms were applied here, other than aksing the staff so explain it in English! And we think we have problems in the life-sciences! An example of the menu can be seen in the photo graphs which also include the delegates the meal and the venue.

First MIBBI workshop 2-3rd April 2008

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The First MIBBI Workshop: Day 1

MIBBI is a registry of scientific experiment reporting guidelines with the idea to foster a foundry of best practice to further develop and encourage modular development and re-use of reporting guidelines. The first workshop is being held at the EBI on the 2nd – 3rd April 2008 and is a relatively closed workshop to those developers and guidelines that are registered on the site. The schedule for day one is a whistle stop tour consisting of 5 min talks (adjusting for an academics interpretation of what 5 minutes means) for all the guidelines that exist, their scope and the people behind them. Due to this I am not going to comment on individual talks. I presented two talks during the day. One on CARMEN and the development of the MINI: Electrophysiology reporting guidelines, and one, standing in for Andy Jones on FuGE.

I tried sharing these slides via google presentation, they looked quite nice. However, wordpress does not seem to allow them to embed. So I put them on slide share instead. These set the tone for the discussions for the afternoon and tomorrow.


AHM day 2

This was a busy day on the booth for me so did not get to attend many talks. I did however attend the Keynote by Professor Tom Kirkwood entitled The Grand Challenge of Population Ageing: e-Science to the Rescue. It was a very interesting talk by a good speaker on the science behind ageing. However the e-Science to the Rescue was very thin. As this was an e-science conference I would have liked to have seen a more emphasis on the e-science. I am familiar with this project and the excellent work on an omics data portal called symba. Unfortunately symba was restricted to a slide or two that were quickly flashed up near the end of the presentation, which I found a bit of a let down.

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All Hands meeting Day 1

I’m a bit late in my posting, just been to busy going to talks and discussing things, anyway. My first session at this years AHM was a workshop on “Issues is Ontology Development and Use. The welcome and workshop overview was presented by Alan Rector. I only caught the end of this introduction, as I was getting my fix of caffeine after travelling all day. The full program for the workshop and the full meeting can be found here. However there were a few presentations that stood out for me. The first one for all the wrong reasons. A talk entitled Ontology building as Practical work:Lessons from CSCW was a talk given on an overhead projector. No chance of power point poisoning tonight. Apparently he has had to step in at
the last minute to give the talk so they are not his slides, and it is starting to show. Oh dear he has given up on some of the slides and is just reading them out, disappointing.

Another talk entitled “A Socio-technical Perspective on Ontology Development in HealthGrids” by Jenny Ure, was interesting and CARMEN got a mention to which is always good. The talk described the alignment of the development of ontologies within similar e-Science projects and the BIRN project for Neuroimaging

Another talk that stood out for me was by Alistair Miles entitled “Collaboration in the value Grid for Semantic Technologies”. Within this talk I heard alot of new terms such as “Value Grids” in collaborating and building ontologies, all which is relevant for my work, and now apparently I am a “Collaborative engineer”. At the end of the talk he also gave a purl for his blog which I though was a nice touch. His post on the workshop which can be found here.

The final session of the workshop was an open discussion session on the main themes of the workshop, some of the discussion points are listed below. Unfortunately due to time there were no definitive answers to these points. However the slant was different from what I have been used to in other ontology workshops in the past where the application and use drives ontology development. However this discussion was more concerned with the computing science development rather than ontology application.

  • How are ontologies developed in practice and why?
  • Who should be involved and how should they work together?
  • How would we deal with disagreement and conflict?
  • What is the right strategy for encouraging adoption?
  • What is the right technical strategy?
  • Do we have the right languages tools, development environments?

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2nd International Digital Curation Conference

The Data Curation Center has just held their 2nd International Digital Curation Conference, in Glasgow. The official DCC blog for the conference tracks the thoughts and discourse over the two days and the full program can be found here. As the conference name suggests, the meeting has the particular focus on different aspects of the digital curation life-cycle including managing repositories, educating data scientists and understanding the role of policy and strategy.

One particular talk I was interested in was “The Roles of Shared Data Collections in Neuroscience”. This was presented by a social scientist, as the results of communications with Neuroscientists. Ironically the shared data collection was called “NeuroAnatomical Cell Repository” a pseudonym to “protect the confidentiality of the participants”, so much for the “shared” component! The general conclusions re-iterated what is already know in the bio-sciences; that more experiments are producing large volumes of heterogeneous data that need to be stored, preserved and presented in a manner that allows the efficient use and re-use of the data. There was particular mention that Neuroscience doesn’t have any data reporting standards, a particular buzz-topic in biological sciences.

As a result of this talk, the issue of how we publish this data was again raised, with the provoking statement from the floor, “we should bypass the traditional journals and publish the data ourselves” (a summation of the statement, not an actual quote). This is an issue I have been hearing more and more at recent conferences and in general discussions, a topic that appears to be gathering momentum. Some discourse has already been presented within this blog on some of these issues.

The open panel session on day two, engaged some interesting discussion and I heard a term which I had never heard before, “Open Data“, put forward by Peter Murray-Rust (University of Cambridge). We have all heard of Open Access publishing, (and should not be publishing any other way), but to date this means open access to the journal publication and not the the data that the publication refers to. In something as simple as a graph in a journal publication, generally the access to the numbers/values, has to be re-calculated via a print-out and a ruler. It would be so much easier (and logical) for re-use, analysis or even review, if the presented image was accompanied by the data (even if this was in an excel spreadsheet).

So in summation, the conference presented numerous issues for consideration by a “data scientist” (this may well be the new name for bioinformaticians). The concept of digital data curation is something that is becoming more prevalent in the life-sciences both at the level of the bench scientist (generating metadata) and the analysis, presentation and preservation of the resulting data. No doubt conferences like the DCC will continue to grow in stature and the issues will be further presented in their newly launched International Journal of Digital Curation.