Archive for category conference

Content, Syntax and Semantics

These are the slides I gave at a DCC workshop entitled, “Digital curation 101″ which aimed to give and overview of what to consider regarding data curation and management in the context of applying for research funding. The presentation starts with definitions of content syntax and semantics, and example of how these concepts are being applied in the life-sciences, specifically proteomics.

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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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MGED by Ally

Ally has completed her comprehensive review of the 11th MGED Society meeting – I feel as if I was actually there.  She also won 3rd place in the best poster competition which she presents SyMBA.

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CARMEN – A Scalable Science cloud

Paul Watson presents a talk on CARMEN a the Google Seattle Conference on Scalability.

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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.

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CFP: Bio-Ontologies 2008: Knowledge in Biology

Call for Papers for Bio-Ontologies 2008. Submissions are now invited Bio-Ontologies 2008: Knowledge in Biology, a SIG at Intelligent Systems for Molecular Biology 2008.

Key Dates to remember:

  • Submission due: Friday 2nd May
  • Notifications: Friday 23rd May
  • Final Version Due: Friday 30th May
  • Workshop: Sunday 20th July

Introduction

Bio-Ontologies has existed as a SIG at ISMB for more than a decade, making it one of the longest running. For this time, Bio-Ontologies has provided a forum for discussion on the latest and most cutting edge research on ontologies. In this decade, the use of ontologies has become mature, moving from niche to mainstream usage within bioinformatics. Following on from last year’s reflective look, this year we are broadening the scope of SIG; we are interested in any formal or informal approach to organising, presenting and disseminating knowledge in biology.

So, for example:

  • Semantic and/or Scientific wikis.
  • Multimedia blogs
  • Folksonomies
  • Tag Clouds
  • Collaborative Curation Platforms
  • Collaborative Ontology Authoring and Peer-Review Mechanisms

are topics which will be of relevance to the SIG, in addition to the more traditional areas for bio-ontologies.

  • Biological Applications of Ontologies
  • Reports on Newly Developed or Existing Bio-Ontologies
  • Tools for Developing Ontologies
  • Use of Ontologies in Data Communication Standards
  • Use of Semantic Web technologies in Bioinformatics
  • Implications of Bio-Ontologies or the Semantic Web for drug discovery
  • Current Research In Ontology Languages and its implication for Bio-Ontologies

Please note, that this year ISCB have made an innovative schedule, holding some of the SIGs DURING ISMB. Bio-Ontologies is on the Sunday parallel to the main conference.

Submissions

Submissions are now open and can be submitted through easychair.
Instructions to Authors

We are inviting two types of submissions.

Short papers, up to 4 pages.
Poster abstracts, up to 1/2 page.

Following review, successful papers will be presented at the Bio-Ontologies SIG. Poster abstracts will be provided poster space and time will be allocated during the day for at least one poster session. Unsuccesful papers will automatically be considered for poster presentation; there is no need to submit both on the same topic.

Organisers

  • Phillip Lord, Newcastle University
  • Susanna-Assunta Sansone, EBI
  • Nigam Shah, Stanford
  • Matt Cockerill, BioMedCentral

Programme Committee

The programme committee, organised alphabetically is:

  • Mike Bada, University of Colorado
  • Judith Blake, Jackson Laboratory
  • Frank Gibson, Newcastle University
  • Cliff Joslyn, Pacific National Laboratory
  • Wacek Kusnierczyk, Norwegian University of Science and Technology
  • Robin MacEntire, GSK
  • Helen Parkinson, EBI
  • Daniel Rubin, Stanford University
  • Alan Ruttenberg, Science Commons
  • Robert Stevens, University of Manchester
  • and the conference organisers.

Templates

Submission templates are available from the Bio-Ontologies website.

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