June 19, 2009

Nettab 2009 Day Three: Semantic Integration

Catania ElephantA brief report (well just some scribbled notes, bullet points and links really) on the third and final day of Network Applications and Tools in Biology (NETTAB) 2009 in Catania, Sicily. There was a special section on Methods and Tools for RNA Structure and Functional Analysis. Disclaimer: RNA mania isn’t really my thing – so the RNA presentations and papers are grossly under-represented in this mini-report (sorry).

  • Keynote: Semantically Integrated eCommunities in Biomedicine: Next-Generation Models of Biomedical Communication, Tim Clark Massachusetts General Hospital and Harvard Medical School, Boston. His presentation opened by asking: What do the following have in common?

    1. Alzheimer’s Disease
    2. Huntington’s Disease
    3. Nicotine Addiction
    4. Schizophrenia
    5. Bipolar Disorder
    6. Autism
    7. Parkinson’s Disease
    8. ALS (Amyotrophic lateral sclerosis)
    9. Neuropathic Pain
    10. Major Depressive Disorder
    11. Cancer (multiple forms)


    1. Highly complex disorders
    2. Much information, incomplete understanding
    3. Inadequate treatment options
    4. Huge cost in human suffering
    5. Multi-factorial causality
    6. Require multi-disciplinary collaboration for progress to understanding and cure

    Tim discussed using The Science Collaboration Framework (SCF) a reusable, semantically-aware toolkit for building on-line communities. These make heavy use of Open Linked Data, controlled vocabularies and  Drupal to build websites to tackle the above disorders. For example pdonlineresearch.org (Parkinson’s Disease), StemBook.org (Harvard Stem Cell Institute) and alzforum.org (Alzheimers) [1]. The controlled vocabulary and ontology approach works well for understood stuff (where named entities are known) but not so good at the outer boundaries of our knowledge. Reusable framework for building web communities, Uses shared ontologies/vocabularies, Open source, freely available.

  • Michaela Guendel (Leaf Bioscience) presented DC-THERA Directory: A Knowledge Management System to Support Collaboration on Dendritic Cell and Immunology Research,  using cell type ontology, dendritic cell ontology, chebi, obi. Project involves Andrea Splendiani, Ciro Scognamiglio and Marco Brandizi
  • GePh-CARD: an information exchange application for an Hub & Spoke Network for Skeletal Dysplasias was presented by M. Mordenti & L. Sangiorgi
  • Panel Discussion: Collaborative and Social Bioinformatics Research and Development: Why, When, Who and How? Alex Bateman, Tim Clark, Duncan Hull and all participants. This panel discussion concentrated on Who? (experts vs. non experts, crowds vs. individuals, how to motivate and reward people to contribute to online communities. community annotation of data only possible when curators cede control of data) and then Where? (open wikis vs. closed ones, private vs. public data, wikis often not suitable for highly structured data, centralised vs. distributed systems)
  • Keynote: Bacterial Phylogeny and Taxonomy in the High-Throughput Sequencing World, Gabriel Valiente
  • Magdalena Musielak (has worked with Piotr Byzia) presented RNA tertiary structure prediction with ModeRNA,
  • Olivier Perriquet presented Improved heuristic for pairwise RNA secondary structure prediction,
  • Giampaolo Bella talked about Analysing microRNA by Theorem Proving. qualitative logic proving before quantitative experimental measures e.g. “shall we go to restaurant” before “how much does it cost”?
  • Mapping miRNA genes on human fragile sites and translocation breakpoints Alfredo Ferro et al.
  • Keynote: Computational challenages in the study of small RNAs Doron Betel, memorial sloan-kettering cancer center
  • microrna.gr. a suite of web based tools for elucidating microrna function was presented by Giorgo L. Papadopoulous, DIANA bioinformatics lab, biomedical Science research center, Alexander Fleming, Vari, Athens, Greece
  • Last but not least there was miRScape: a cytoscape plugin to annotate biological networks with microRNAs

The Tenth NETTAB (2010) Workshop will be in Rome, where the theme will be Oncology Bioinformatics and will be held at the end of  May or beginning of  June 2010.


  1. Das, S., Girard, L., Green, T., Weitzman, L., Lewis-Bowen, A., & Clark, T. (2009). Building biomedical web communities using a semantically aware content management system Briefings in Bioinformatics, 10 (2), 129-138 DOI: 10.1093/bib/bbn052

August 7, 2007

Scifoo: Geek Out! Le Geek, C’est Chic…

Deepak Singh and Euan Adie

As well as big famous superstars at Science Foo Camp (scifoo), there is a chance to meet and “geek out” with younger engineers and scientists like Vince Smith, Aaron Schwartz and Vaughan Bell.

Aaron Schwartz and the open library project

On Sunday at scifoo, Aaron (of archive.org) gave a quick demo of the Open Library. Currently this project is taking books that are out of print and not in other book catalogues like Amazon, and making them available online. They are intending to move into archiving scientific journals, so watch that space. I’ve always wondered how the internet archive survived financially, and managed all its interesting projects (like the open library). It’s all funded by some bloke called Brewster Kahle. They provide some great services, like hosting digital artifacts for free, see http://www.archive.org/create/.

Vince Smith, Museums and Drupal

Vince Smith is a “cyber-taxonomist” at the Natural History Museum in London. He’s a world expert on parasitic lice, and uses a multi-site installation of Drupal, see vsmith.info (Hmmm, that drupal skin looks familiar…). Vince uses a drupal module for bibliographic citations, called biblio, looks handy. It’d be nice to have it on nodalpoint? Anyway, anytime spent looking around Vince’s site is time well spent.

Vaughan Bell, Mind Hacker

Vaughan Bell is a clinical psychologist. We chatted about wikipedia and science, as demonstrated by Schizophrenia. He’s also a contributor to a book on MindHacks and blogs at mindhacks.com. My suitcase is full of free O’Reilly book-schwag I filled my boots with on Friday, one of which is Vaughan’s book. Looks like it will be a good read on the plane home, because my brain is in need of some serious “optimisation”.

(Two more geeks, pictured right, but regular nodalpoint readers will know all about them already, Deepak Singh and Euan Adie.)

Theres plenty more I could blog about scifoo, but I’m all foo-ked up, geeked out and mashed-up. It’s time to go home. For more scifoo blogging see www.technorati.com/tags/scifoo, www.nature.com/scifoo and network.nature.com/blogs/tag/scifoo.


  1. Aaaaah: Freak Out! Le Freak, C’est Chic…

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