Monday, November 23, 2009

Government and Open Source Software

A colleague of mine is having some difficulties getting an Open Source solution to be made available within his government organization. In providing support to him, I've collected the below resources. Of particular interest is the 2007 Government Open Source Policies from the Center for Strategic and International Studies, listing the Open Source policies of hundreds of national, state/province/territory and local governments (including Canada's).

Open Source and Data Sharing questions in UK Parliament (Nov 12 2009)

It was very interesting to recently discover this Hansard exchange from the UK parliament dated Nov 12 2009 involving Open Source and sharing data:

House of Commons Hansard Written Answers for 12 Nov 2009

Public Bodies: Databases

Mr. Maude: To ask the Minister for the Cabinet Office what steps her Department is taking to facilitate data sharing among public sector bodies. [299480]

Angela E. Smith: The Ministry of Justice is the lead Department on data sharing. The Cabinet Office supports technical elements of secure data handling and ensures that considerations of Data Sharing informs our work to promote more joined up public services.

Sharing data securely is a requirement of the Data Handling Review, which all public bodies must adhere to.

Public Sector: ICT

Mr. Maude: To ask the Minister for the Cabinet Office what assessment has been made of the levels of compliance with her Department's guidance on public sector open source software procurement; and what steps are being taken to ensure compliance. [299407]

Angela E. Smith: The Open Source, Open Standards and Re-use Action Plan was published in February 2009 and is Government policy.

The Office of Government Commerce (OGC) is currently developing guidance for the procurement of open source, working with departments and local authorities that have successfully implemented open source applications, to share best practice and effective methods for procurement. The basis of the guidance has been prepared and material based on practical experience is now being sought from industry and government bodies to enhance the content.

The Cabinet Office does not gather centralised data regarding software procurement.
I'm glad someone's parliament is at least talking about these issues.

Wednesday, November 18, 2009

Opening government funded research to improve research, teaching and learning in higher education

The report Harnessing Openness to Improve Research, Teaching and Learning in Higher Education (A Report by the Digital Connections Council of the Committee for Economic Development Committee, 2009 ISBN #0-87186-184-7) has some very relevant sections dealing with Open Access and Open Data in the context of higher education and the research process:

  • Chapter 5. Openness in Higher Education: Changes in Research
    • a. Resistance to Greater Openness
    • b. Openness and Open-Access Journals
    • c. Digital Repositories
    • d. Educating Faculty Members on Their Intellectual Property Rights
    • e. Openness and Commercial Support of Research
    • f. Access to Government-Funded Research Results
    • g. Openness and University Libraries
    • h. Openness and Academic Presses
    • i. Openness and Technology Transfer
Of particular interest to those who - perhaps at a more general level - are working on getting better access to government funded research, are the following recommendations on this particular issue:
  • f. Access to Government-Funded Research Results
    Recommendations
    Governments should:
    • Retain the existing requirements of the NIH public-access policy regarding the results of NIH-funded research (public availability within 12 months of publication).
    • Stimulate research and increase the pace of innovation
      by extending the NIH public-access policy to cover all non-classified research funded by the 11 federal agencies providing over $100 million each in research support.
    • Extend the NIH public-access policy, under appropriate conditions, to primary data resulting from federally funded research and data gathered in support of government regulatory activities.
    • Extend the NIH public-access policy to publicly funded research at institutions of higher education at the state, and local levels.
    • Adopt policies that promote the accessibility and utilization of all non-classified government procedures and processes, data and information products (e.g. databases, publications, audio and video products etc.) as well as materials held in government-funded museums and collections. Lower, to the extent practicable, barriers to access and use, including permission and attribution requirements and technological barriers. Consider the utilization of standardized formats and metadata to facilitate searching and use. (Policies should neither favor one commercial entity over another nor commercial entities over noncommercial entities.)
    • Develop long-term plans and policies for ongoing permanent public access to government information in whatever form, taking into account the fragility of digital media and the format migration that has impeded access.

Thanks to Bill St. Arnaud for this info.

Monday, November 16, 2009

Symposium on the Data Sharing Plans and on the Scientific Benefits of Data Sharing in GEOSS

Today in Washington. D.C, the CODATA organized Symposium on the Data Sharing Plans and on the Scientific Benefits of Data Sharing in GEOSS was held. Among other things, it looked at the draft GEOSS data sharing plan:

The Plan, now endorsed by 80 government Members and 56 Participating Organizations, highlights the following GEOSS Data Sharing Principles:
  1. There will be full and open exchange of data, metadata, and products shared within GEOSS, recognizing relevant international instruments and national policies and legislation.
  2. All shared data, metadata, and products will be made available with minimum time delay and at minimum cost.
  3. All shared data, metadata, and products being free of charge or no more than cost of reproduction will be encouraged for research and education.
Programme:
  • Part One: Implementing the GEOSS Data Sharing Principles
    • How We Got There and Where We're Going. Beth Greenaway. UK Environmental Observation Network
    • An Overview of the Key Substantive Provisions of the Implementation Guidelines. Robert Chen, of the Implementation Guidelines CODATA and Columbia University
    • Panel Discussion with the Symposium Participants Moderated by Roberta Balstad
  • Part Two: The Scientific Benefits of Data Sharing
    • Data Sharing and Innovation. Christopher Tucker, Open Geospatial Consortium (OGC) Board
    • Understanding Ecosystems and Their Services. Anthony Janetos, Director, Joint Global Change Research Inst., PNL/University of Maryland
    • Earthquakes, Tsunamis and Nuclear Explosion: Open Data Exchange for Research and Monitoring. David Simpson, President, IRIS in Seismology

Disclaimer: I am a member of the Canadian National Committee (CNC) for CODATA

frAgile programming...

Ravi Mohan has posted to his blog, Pin Dancing, a provocative (and likely correct) evaluation of the Agile/xtreme/lean programming wave we have seen over the last couple of years ("Let the Agile Fad Flow By" - Sept 26 2009). Enjoy.

Tuesday, November 10, 2009

Data Life Cycle Patterns in the Life Sciences

The UK Research Information Network (RIN) and the British Library (BL) have produced an amazing report looking at the patterns of flow of data in its production and tranformation in the research process of life scientists.

Patterns of information use and exchange: case studies of researchers in the life sciences. A report by the Research Information Network and the British Library November 2009.
They have seven case studies that look at the data lifecycles of data for researchers in the following life science disciplines:
  • Animal genetics and animal diseases
  • Transgenesis in the chick and development of the chick embryo
  • Epidemiology of zoonotic diseases
  • Neuroscience
  • Systems biology
  • Regenerative medicine
They have extended Chuck Humphrey's data lifecycle model, and use this extended model to illustrate how the data lifecycles are expressed in these different disciplines:



The diagrams (below) for the different disciplines are very revealing, and show the great deal of diversity in and between these disciplines, as well as the complexity within many of these areas.

In doing this analysis, the researchers found that an effective representation of this information involved the following two axes:
  • "the volume of data being handled"
  • "the complexity or heterogeneity of that data"
The researchers plotted the seven disciplines into this space, shown in the following diagram:

Discipline data lifecycle diagrams:
  • Animal genetics and animal diseases


  • Transgenesis in the chick and development of the chick embryo

  • Epidemiology of zoonotic diseases

  • Neuroscience
  • Systems biology (Computing-bases and Lab-based)



  • Regenerative medicine


  • Regenerative medicine

Note: All of these diagrams presented here are from the publication, which has the following license: Creative Commons Attribution-Non-Commercial-Share-Alike 2.0 UK: England and Wales License.

Thursday, November 05, 2009

The Future of Science: Semantic Web Applications in Scientific Discourse

For those who want to take a glimpse at where science and scientific discourse are going, take a look at some of the papers at this workshop:

Workshop on Semantic Web Applications in Scientific Discourse, October 26, 2009, Proceedings), part of The 8th International Semantic Web Conference (ISWC 2009)
  • Keynote: Enabling Semantic Publication and Integration of Scientific Information
    David Shotton. Presentation.

  • A Short Survey of Discourse Representation Models
    Tudor Groza, Siegfried Handschuh, Tim Clark and Simon Buckingham Shum
    Paper Presentation

  • Strategic Reading and Scientific Discourse
    Allen Renear and Carole Palmer
    Paper

  • 'Confortation': about a new qualitative category for analyzing biomedical texts
    Delphine Battistelli, Antonietta Folino, Patricia Geretto, Ludivine Kuznik, Jean-Luc Minel and Florence Amardeilh
    Paper Presentation

  • Hypotheses, Evidence and Relationships:The HypER Model of Representing Scientific Knowledge
    Anita de Waard, Simon Buckingham Shum Annamaria Carusi, Jack Park, Matthias Samwald and Agnes Sandor
    Paper Presentation

  • SWAN/SIOC: Aligning Scientific Discourse Representation and Social Semantics
    Alexandre Passant, Paolo Ciccarese, John Breslin and Tim Clark
    Paper Presentation

  • Harnessing the Power of the Community in a Library of Biomedical Ontologies
    Natasha Noy, Michael Dorf, Nicholas Griffith, Csongor Nyulas and Mark Musen.
    Paper Presentation

  • myExperiment: An ontology for e-Research
    David Newman, Sean Bechhofer and David De Roure
    Paper Presentation

  • System Description: Reaching Deeper into the Life Science Bibliome with CORAAL
    Vit Novacek, Tudor Groza and Siegfried Handschuh
    Paper Presentation

  • Nano-Publication in the e-Science Era
    Barend Mons and Jan Velterop.
    Paper Presentation