[OWW-SC] Open Science Talk Nov 4 by Cameron Neylon

[Austin Che]

    Please let whoever you think might be interested know about the
    following. It will be a 30 minute talk followed by 30 minutes of
    discussion about openness in general.

    News team: we might want to have a news highlight about this on
    the front page.
    
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    http://openwetware.org/wiki/Seminar_Series/Cameron_Neylon
    
    3:30pm, Sunday November 4th, 2007
    MIT Stata Center, 32-155
    Organized in conjunction with iGEM
    Speaker: Cameron Neylon
    
    Title: A Beginner's Guide to Open Science (not for beginners but by
    beginners)

    Abstract:    
    The modern biochemistry or molecular biology laboratory generates
    large quantities of data that are generally stored across multiple
    computers attached to multiple instruments. Much of this data is
    never published and the majority languishes on old computers and
    is ultimately lost. At a local level this is a frustration for
    investigators who will often struggle to obtain specific pieces of
    data produced in their own laboratory. On a larger scale this is
    becoming a much more serious issue with the obligation of
    researchers to funding bodies to both preserve research data and
    make it available to other users increasingly becoming a formal a
    condition of publicly funded grants. Systems are required that can
    capture and preserve data along with sufficient information and
    metadata to make it possible for others to use this data.

    In parallel with this a movement is growing within the research
    community that advocates greater openness in providing both the
    raw data from published studies as well as making available the
    large quantities of data that are never published. The logical
    extreme of this approach is Open Notebook Science [1], pioneered
    at Drexel University [2], where the researcher's laboratory
    notebook is made available on the internet as it is
    recorded. Achieving the aims of Open Notebook Science also
    requires systems which can capture data and provide it in a useful
    format. In addition these systems must make the data visible to
    relevant online searches.

    We are developing and using an electronic laboratory notebook
    based on a Blog format to capture experimental data in a
    biochemistry laboratory [3,4]. Within the system each sample is
    recorded in a single post. Analysis and manipulations of the
    sample are recorded in separate posts with links back to the input
    sample and forward to any products. All the information is made
    immediately available on the Web as it is recorded. The Blog
    engine has been specially built in house and has a number of
    features designed to enable and encourage the effective capture of
    data and metadata in the environment of a biochemistry
    laboratory. I will describe the Blog system and our evolving
    approach to capturing metadata as well as the process of
    integrating this with other web services to provide an open
    environment for recording work in the laboratory, laboratory
    materials, and validated procedures. The challenges and problems
    encountered in reconciling the twin aims of capturing data and
    making it available and readable will also be discussed along with
    the similarities and differences emerging between different
    approaches to Open Notebook Science [2,5,6].

    [1] http://drexel-coas-elearning.blogspot.com/2006/09/open-notebook-science.html
    [2] http://usefulchem.wikispaces.com/
    [3] http://chemtools.chem.soton.ac.uk/projects/blog/blogs.php/blog_id/10
    [4] http://chemtools.chem.soton.ac.uk/projects/blog/blogs.php/blog_id/13
    [5] http://www.jeremiahfaith.com/open_notebook_science/
    [6] http://www.michaelbarton.me.uk/

    Biography:
    Cameron studied for a first degree in Biochemistry at the
    University of Western Australia before moving to the Research
    School of Chemistry at the Australian National University to study
    for a PhD in protein chemistry and molecular biology. After his
    doctoral studies he moved to the United Kingdom to take up a
    Wellcome Trust International Travelling Fellowship at the
    University of Bath to develop a library of constrained peptides as
    potential activators of 7-transmembrane receptors.

    In 2001 he moved to the School of Chemistry at the University of
    Southampton as Lecturer in Chemical Biology and in 2005 he took up
    a joint appointment as Senior Scientist in Biomolecular Sciences
    at the ISIS Neutron Scattering Facility located within the STFC
    Rutherford Appleton Laboratory. Current areas of research include
    the development of new methods for protein labelling and the
    synthesis of protein conjugates, experimental and computational
    approaches studies of high throughout nucleic acid sequence
    analysis, and the the development of complementary analytical
    methods for probing the structure and dynamics of proteins and
    protein-ligand complexes in solution. In addition to these
    experimental studies the combination of high throughput
    methodology and working on two sites has led to a developing
    interest in open approaches to science and electronic lab
    notebooks being developed in collaboration with the group of
    Professor Jeremy Frey.