1. The document summarizes the speaker's wish list and vision for improving scientific publishing and communication. The speaker advocates for more open access to literature and data, better integration of literature and data, and ensuring reproducibility through sharing of workflows, source code, and data. 2. The speaker discusses experiments with rich media formats like video to enhance scholarly communication. The goal is to leverage new technologies and better link literature, data, and methods. 3. The current reward system in academia does not adequately incentivize open and reproducible science. New models are needed that reward things like maintaining databases, curating data, and developing community resources.

1. One Scientist’s Wish List for Scientific Publishers Philip E. Bourne University of California San Diego [email_address] www.sdsc.edu/pb http://www.slideshare.net/pebourne Conference of ACS Editors Jan 6, 2012, La Jolla CA

3. What Drives Me…. The Story of Meredith

8. The Dream Can Only be Realized in the Context of the Complete Research Enterprise Literature Data Methods

9. My Current Reality http://www.flickr.com/photos/51282757@N05/5585299226/lightbox/

10. Let Me Try and Illustrate What is Possible Through Our Own Little Contributions

11. Much of What We Try and Do Leverages Open Access Content 2008 Open Access: Taking Full Advantage of the Content PLoS Comp. Biol. 4(3) e1000037

13. Literature: Semantically Enriched Version of PubMed Central Literature Data Methods http://biolit.ucsd.edu ; NAR 2008 36(S2) W385-389

15. Data & Literature: Integration www.rcsb.org/pdb/explore/literature.do?structureId=1TIM Literature Data Methods BMC Bioinformatics 2010 11:220

17. Literature: Knowledge Discovery Shared Function Literature Data Methods Immunology Literature Cardiac Disease Literature

18. Lets Turn Our Attention to Data ….

22. .. And Finally Methods

25. Methods: Workflow Tools Might be the Answer? Taverna Wings Literature Data Methods

27. Methods: Yes The Workflow is Real Literature Data Methods

29. And Now for Something Completely Different http://www.scivee.tv

30. Experiments in Rich Media Mashups http://www.scivee.tv

31. Pubcast – Video Integrated with the Full Text of the Paper http://www.scivee.tv

32. Rich Media as Scholarship Products Application Product Primary Customers Journals PubCast Journals, publishers, societies Meetings PosterCast Societies, conference orgs. SlideCast Comm. PaperCast Societies, journals Podcast SlideCast Education PosterCast Societies, universities SlideCast Books BookCast Publishers, book sellers http://www.scivee.tv

33. Android iPhone Windows Phone 7 Step 1 presenter starts PowerPoint Step 2 presenter starts recording on smart phone Step 3 presenter stops recording and initiates upload Slides Website Step 5 slides and podcast are automatically synchronized Sync File Podcast Step 6 listener plays back synchronized presentation Podium Capture Mac PC Step 4 slides are uploaded http://www.scivee.tv

34. Nothing is Going to Change Unless The Reward System Changes The Right Thing To Do Reward P.E. Bourne 2011 Ten Simple Rules for Getting Ahead as a Computational Biologist in Academia. PLoS Comp. Biol. 7(1) e1002001.

36. In Summary: I Do Not Want to Do Any of This – I Want You to Do It P.E. Bourne 2010 What Do I Want from the Publisher of the Future? PLoS Comp Biol 6(5): e1000787

37. What Does That Mean? The “Publisher” becomes Part of the Scientific Workflow Scientist Idea Experiment Data Conclusions Publish Laboratory Publisher Maybe The Line is Somewhere Else? uzar.wordpress.com

38. Maybe The Line is Somewhere Else? Scientist Idea Experiment Data Conclusions Publish Laboratory Publisher Institution? Lab Notebook ?

39. Maybe The Line is Somewhere Else? Scientist Idea Experiment Data Conclusions Publish Laboratory Publisher Institution? Lab Notebook ?

40. Questions? [email_address]