Wednesday, August 20, 2008

Journal of Visualized Experiments now indexed by PubMed

The Journal of Visualized Experiments (JoVE) - which publishes research video-articles - is now indexed by PubMed, as reported in the JoVE blog.


  • Visualize This! Interview with Moshe Pritsker, co-founder and editor-in-chief of JoVE [2008 Feb]

  • Troy, T., Arabzadeh, A., Enikanolaiye, A., Lariviere, N., Turksen, K. (2008). Immunohistochemistry on Paraffin Sections of Mouse Epidermis Using Fluorescent Antibodies. Journal of Visualized Experiments DOI: 10.3791/552. A JoVE video article from University of Ottawa and Ottawa Health Research Institute (I work in the Ottawa area).

NSF: Expeditions in Computing Awards

The U.S. National Science Foundation (NSF) has announced the four 2007 grant ($10M over 5 years) awardees of its Expeditions in Computing. The funded projects are:

Cyberinfrastructure for biological sciences

This paper takes a more semantic web and forward looking view than recent cyberinfrastructure articles:

  • Stein, L. D. (2008).Towards a cyberinfrastructure for the biological
    sciences: progress, visions and challenges Nat Rev Genet, 9(9), 678-688. DOI: 10.1038/nrg2414

Things like Semantic Web Pipes - missing from the article - can be found on the wiki page for the article (Thanks Matthias Samwald).

Related recent articles:
  • Goble, C., Stevens, R. (2008). State of the nation in data integration for bioinformatics. Journal of Biomedical Informatics DOI: 10.1016/j.jbi.2008.01.008

  • Stockinger, H., Attwood, T., Chohan, S.N., Cote, R., Cudre-Mauroux, P., Falquet, L., Fernandes, P., Finn, R.D., Hupponen, T., Korpelainen, E., Labarga, A., Laugraud, A., Lima, T., Pafilis, E., Pagni, M., Pettifer, S., Phan, I., Rahman, N. (2008). Experience using web services for biological sequence analysis. Briefings in Bioinformatics DOI: 10.1093/bib/bbn029

  • Garciasanchez, F., Fernandezbreis, J., Valenciagarcia, R., Gomez, J., Martinezbejar, R. (2008). Combining Semantic Web technologies with Multi-Agent Systems for integrated access to biological resources. Journal of Biomedical Informatics DOI: 10.1016/j.jbi.2008.05.007

  • Belleau, F., Nolin, M., Tourigny, N., Rigault, P., Morissette, J. (2008). Bio2RDF: Towards a mashup to build bioinformatics knowledge systems. Journal of Biomedical Informatics DOI: 10.1016/j.jbi.2008.03.004

  • Sagotsky, J.A., Zhang, L., Wang, Z., Martin, S., Deisboeck, T.S. (2008). Life Sciences and the web: a new era for collaboration. Molecular Systems Biology, 4 DOI: 10.1038/msb.2008.39

Tuesday, August 12, 2008

"The Use And Misuse Of Bibliometric Indices In Evaluating Scholarly Performance"

Ethics In Science And Enviromental Politics Vol. 8, No. 1, Special Issue: The Use And Misuse Of Bibliometric Indices In Evaluating Scholarly Performance is an extensive set of papers on bibliometric indices. I have as yet to read them, but they look interesting and significant:

  • Browman, H., Stergiou, K. (2008). Factors and indices are one thing, deciding who is scholarly, why they are scholarly, and the relative value of their scholarship is something else entirely. Ethics in Science and Environmental Politics, 8, 1-3. DOI: 10.3354/esep00089

  • Campbell, P. (2008). Escape from the impact factor. Ethics in Science and Environmental Politics, 8, 5-7. DOI: 10.3354/esep00078

  • Lawrence, P. (2008). Lost in publication: how measurement harms science. Ethics in Science and Environmental Politics, 8, 9-11. DOI: 10.3354/esep00079

  • Todd, P., Ladle, R. (2008). Hidden dangers of a "citation culture". Ethics in Science and Environmental Politics, 8, 13-16. DOI: 10.3354/esep00091

  • Taylor, M., Perakakis, P., Trachana, V. (2008). The siege of science. Ethics in Science and Environmental Politics, 8, 17-40. DOI: 10.3354/esep00086

  • Cheung, W. (2008). The economics of post-doc publishing. Ethics in Science and Environmental Politics, 8, 41-44. DOI: 10.3354/esep00083

  • Tsikliras, A. (2008). Chasing after the high impact. Ethics in Science and Environmental Politics, 8, 45-47. DOI: 10.3354/esep00087

  • Zitt, M., Bassecoulard, E. (2008). Challenges for scientometric indicators: data demining, knowledge-flow measurements and diversity issues. Ethics in Science and Environmental Politics, 8, 49-60. DOI: 10.3354/esep00092

  • Harzing, A., van der Wal, R. (2008). Google Scholar as a new source for citation analysis. Ethics in Science and Environmental Politics, 8, 61-73. DOI: 10.3354/esep00076

  • Pauly, D., Stergiou, K. (2008). Re-interpretation of ‘influence weight’ as a citation-based Index of New Knowledge (INK). Ethics in Science and Environmental Politics, 8, 75-78. DOI: 10.3354/esep00090

  • Giske, J. (2008). Benefitting from bibliometry. Ethics in Science and Environmental Politics, 8, 79-81. DOI: 10.3354/esep00075

  • Butler, L. (2008). Using a balanced approach to bibliometrics: quantitative performance measures in the Australian Research Quality Framework. Ethics in Science and Environmental Politics, 8, 83-92. DOI: 10.3354/esep00077

  • Bornmann, L., Mutz, R., Neuhaus, C., Daniel, H. (2008). Citation counts for research evaluation: standards of good practice for analyzing bibliometric data and presenting and interpreting results. Ethics in Science and Environmental Politics, 8, 93-102. DOI: 10.3354/esep00084

  • Harnad, S. (2008). Validating research performance metrics against peer rankings. Ethics in Science and Environmental Politics, 8, 103-107. DOI: 10.3354/esep00088

Thanks to Gerry McKiernan.

Thursday, August 07, 2008

Microsoft Research Faculty Summit 2008: Publishing and Research Tools for Academics

The Microsoft Research Faculty Summit 2008 included Publishing and Research Tools for Academics that allows for archival annotation and structuring of Microsoft software produced documents, as well as supporting PubMed Central format.

Additional sessions of interest:

  • The Cyberspace Connection – Impact on Individuals, Society, and Research
  • New Developments in Scholarly Communication
  • Reflections on Directions in Artificial Intelligence
  • What Will Be the Impact of Cloud Services on Science?
  • Spotlights on Interdisciplinary Artificial Intelligence Research
  • AI, Sensing, and Optimized Information Gathering: Trends and Directions
  • Ontological Myths: Reducing the Confusion
  • Social Networking and Semantics
  • Toward Situated Interaction
  • Statistical Machine Translation Research at Microsoft Research
  • Interactive Machine Learning: Challenges, Methods, and Applications
  • Information Extraction from Documents and Queries
  • Contexts in Computer Science Education
  • The Future of Research Clouds
  • REAssess: Resources for Educational Assessment
  • The Broader Impact of eScience — Discussion Panel
    • The Broader Impact of eScience. Daron G. Green
    • eScience: Data, Computing, and Crowds. Peter Lee
    • Implications of eScience for Science and Society: A View from Genomics. Adam Siepel
    • eScience: Promoting Public Engagement. Wei Wang
    • eScience for All: Not If, But When. Jeannette M. Wing
  • Artificial Intelligence Theory and Practice: Hard Challenges and Opportunities Ahead
  • National Engagements for Promoting Women in Computing
  • Games for Learning: Understanding What Makes an Effective Game for Learning
  • Networks, Social Science, and Education: Teaching, Linking, and Thinking About Connection
    • Social Visualization: Communication, Signal, or Cue? Karrie Karahalios
    • Using Social Network Sites in Education. Cliff Lampe
  • CmapTools: From Meaningful Learning to a Network of Knowledge Builders
  • Pushing and Pulling Information From the Mexican Dataspace
  • Participation in a World of Choice: Microsoft and Open Source

arXiv readership/citation bias examined

the scholarly kitchen has a very interesting discussion ("The importance of being first") that looks at the various biases impacting article readership at arXiv. Based on two recent articles[1,2], biases introduced by the email announcement schedule (sent out at 4PM North American Eastern Time) of arXiv (geographical bias) as well author game- or evolutionary theory strategies of self-promotion (Submit as close to 4pm so as to appear at the top of the email announcement, thus increasing readership...) can significantly change the readership and citation rate of an article. Interesting and clearly something that needs to be reduced/taken-in-to-account/monitored at similar sites.

I would be surprised if there weren't already EBay sniping-(bidding)-bot-like bots out there that can automatically submit articles to arXiv in the last 10 seconds of 4pm.

[1]Dietrich, J.P. (2008). The Importance of Being First: Position Dependent Citation Rates on arXiv:astro-ph. Publications of the Astronomical Society of the Pacific, 120(864), 224-228. DOI: 10.1086/527522

[2]Dietrich, J.P. (2008). Disentangling Visibility and Self-Promotion Bias in the arXiv:astro-ph Positional Citation Effect. Publications of the Astronomical Society of the Pacific, 120(869), 801-804. DOI: 10.1086/589836

Wednesday, August 06, 2008

Open Access / Data release discussion at Genome Canada Conference

It is encouraging to see a session at the upcoming Genome Canada conference (Genome Canada Third International Conference, 2020 Vision: The Impact of Science on Society, Vancouver, October 22 - 24, 2008) entitled "Commercialization, Data Release, and Open Access: Incompatible Objectives?".

Other sessions at the conference:

  • Human Genetic Variation
  • Science should be on Tap not on Top: the Role of Government Science Advisers
  • A New Paradigm for Drug Discovery (Round table discussion)
  • Green Genomics
  • Genomics of Childhood Diseases
  • Stem Cells
The session: "Science should be on Tap not on Top: the Role of Government Science Advisers" is to be chaired by Arthur Carty, the former president of the National Research Council (NRC), and the former science advisor to the Canadian prime minister. I was unaware that Dr. Carty had recently been named the first executive director of the Waterloo Institute of Nanotechnology (web site??), as indicated in this news release from April, 2008. The construction of a $160M building (The Mike and Ophelia Lazaridis Quantum-Nano Centre) to house the institute has begun. The building will also house the Institute for Quantum Computing - whose chairman is Tom Brzustowski, the former president of NSERC - and the undergraduate program in nanotechnology engineering. It looks like these two scientists and science leaders have returned to the University of Waterloo, back to where they were when I was attending the university in the mid-late 1980s.


Disclosure: I am employed by the NRC.

Tuesday, August 05, 2008

Some diverse Open Access references

Here are a number of fairly recent Open Access (OA) references that I have collected that need a home. They are from a number of different perspectives, certainly beyond the usual science, technology, medicine (STM) focus of most of my OA postings, and include Middle East Studies, law publishing, OA activities in China and South Asia, and even Bakhtinian dialogism! I hope they are useful:

Open Access to calculated chemical properties of 12M substances

ChemStar (Computed Molecular Data) is an Open Access database of the calculated chemical properties of over 12M substances from PubChem. The process - which demands significant computing power - was done is a distributed fashion using JavaRMI and is described in the paper below. The properties are calculated using three different methods: JChem, JOELIB and MOE. The site allows the perusal of the properties, with a Marvin-based applet for viewing structures. The Java sourcecode for the distributed computing is available.

Karthikeyan, M., Krishnan, S., Pandey, A.K., Bender, A., Tropsha, A. (2008). Distributed Chemical Computing Using ChemStar: An Open Source Java Remote Method Invocation Architecture Applied to Large Scale Molecular Data from PubChem. Journal of Chemical Information and Modeling, 48(4), 691-703. DOI: 10.1021/ci700334f