Tag: open science

New #UCDavis Open Science Group & OpenWetWare page

Just got an email about this group from Carl Boettiger and thought I would help spread the word. If interested in open science and affiliated with Davis please sign up:

I just met some students recently who were talking about creating an Open Science group at UC Davis. Thought you might be interested in joining their mailing list: openscience@ucdavis.edu

email listproc@ucdavis.edu with
subscribe openscience firstname lastname
in the body.

Some more info here: http://openwetware.org/wiki/UC_Davis_Open_Science

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

GlaxoSmithKline opening up malaria data a wee bit, but more needed

Robert Langreth in an article at Forbes.Com on January 20 (GlaxoSmithkline’s Malaria Plan: Limit Profits, Open Labs) reports that Glaxo Smith Kline is becoming a bit more open with their data on malaria drug/vaccine development.  Apparently, they plan to open up their labs and some of their data to non profit collaborators such as Emory University.  Sounds like this could be a good first step.  But if they really want to advance malaria vaccine research, perhaps they should release their data to everyone? I get that they want/need to make a profit, but if they want to try and get credit for being open, I think they really should jump into the deep end and do something radical.  Just sharing bits and pieces of data with a few labs is not a particularly stunning move.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

More on the PLoS Special Collection on the Genomic of Emerging Infectious Diseases

In case people have not seen in. There is a new collection out from PLoS on the Genomics of Emerging Infectious Diseases. The collection, edited by me and Catriona MacCalum, one of the PLoS Biology Editors. It was sponsored by Google.Org who have a growing interest in emerging infectious diseases. Also heavily involved were Carol Featherstone a freelance writer/editor and Maggie Brown the copy editor.


An Editorial by me and Catriona describing the collection is here: PLoS Biology: Genomics of Emerging Infectious Disease: A PLoS Collection

The papers in the collection are listed below. It truly is an amazing collection of papers all on genomics of emerging infectious diseases and all completely open. Take the material from these papers. Reprint it. Reuse us. Mash it up. Use the figures. And most of all, help in the fight against emerging infectious diseases. Thanks to all the authors, all the PLoS folks (especially Catriona) and all the Google.Org people for working on this. And also thanks to Dr. Kiki for handling the interview for the podcast about the series which is available here.

http://www.flickr.com/apps/slideshow/show.swf?v=71649

Some more on the series from the web:

Eisen, J., & MacCallum, C. (2009). Genomics of Emerging Infectious Disease: A PLoS Collection PLoS Biology, 7 (10) DOI: 10.1371/journal.pbio.1000224

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

RIN/NESTA open science case studies project

Just got this email ….

RIN/NESTA open science case studies project

The Research Information Network (RIN) and the National Endowment for Science, Technology and the Arts (NESTA) are looking to fund a series of case studies which will look at what motivates researchers to work in an open way with their data, results and protocols, and whether there are advantages to working this way. The case studies will also examine the disincentives and barriers to such ‘open science’ methods. The RIN and NESTA are making available up to £15,000 for this project, which is intended to run from October 2009 until January 2010.

Expressions of interest are sought, in the form of an outline statement, on not more than a single sheet of A4, indicating the scope and rational of the proposal, the research methodology likely to be used and suggestions of case studies to be examined. The deadline is 9 September 2009. For more information visit http://www.rin.ac.uk/open-science

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Nice Video on Science 2.0 w/ Stephen Friend, @jimmy_wales, John Wilbanks & @timoreilly (via @Boudicca) #openscience

Embedding the short and long videos here. Hat tip to Lisa Green for pointing these out.

http://vimeo.com/moogaloop.swf?clip_id=6077540&server=vimeo.com&show_title=1&show_byline=1&show_portrait=0&color=&fullscreen=1

Making the Web Work for Science – Short from Jordan Mendelson on Vimeo.

http://vimeo.com/moogaloop.swf?clip_id=6087817&server=vimeo.com&show_title=1&show_byline=1&show_portrait=0&color=&fullscreen=1

Making the Web Work for Science – Full from Jordan Mendelson on Vimeo.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

They copied my posting and I like it …

To me, science is about the spread of ideas and knowledge. And as long as I get credit for my ideas and my writing, I am more than happy for people to run with them. I feel the same way about my blog. Thus I was happy when a blog called The Reef Tank said they wanted to include more science about marine biology there and wanted to cross post some of my marine focused postings.  And they have done the first one here.  All the power to them for wanting to include more science there and happy they are giving my postings another life …

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Joe Derisi and Open Science featured on Voice of America

Well, I already gave him one of my awards, so what else could he do?  Anyway, always good to see Open Science getting promoted and nice to see Voice of America running a story on Joe Derisi after his Heinz Award and featuring this openness (listen to an MP3 of the radio story here).  And they even interviewed me because of my blog about him.  Blogs and the “real” news merge closer and closer every day.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Open Science Required Reading: MSNBC on "Era of scientific secrecy nears its end"

There is a must read out there about Open Science. Robin Lloyd has a excellent article on Open Science (Era of scientific secrecy nears its end) posted at MSNBC. I am not sure whether this was originally written for MSNBC or not nor the whole history of the piece. But the article discusses some of the issues associated with Open Science.
It has some good sections like:

The openness at the technological and cultural heart of the Internet is fast becoming an irreplaceable tool for many scientists, especially biologists, chemists and physicists — allowing them to forgo the long wait to publish in a print journal and instead to blog about early findings and even post their data and lab notes online. The result: Science is moving way faster and more people are part of the dialogue

It also lists some of the aspects of Open Science including

  • Blogs where “scientists can correspond casually about their work long before it is published in a journal”;
  • Social networks “that are scientist friendly such as Laboratree and Ologeez”
  • Sharable sites like “GoogleDocs and wikis which make it easy for people to collaborate via the Web on single documents”
  • Citation sharing sites like “Connotea that allows scientists to share bookmarks for research papers”
  • Preprint servers “such as Arxiv, where physicists post their “pre-print” research papers before they are published in a print journal”
  • OpenWetWare “which allows scientists to post and share new innovations in lab techniques”
  • Video sharing sites like “The Journal of Visualized Experiments, an open-access site where you can see videos of how research teams do their work”
  • Sequence databases like “GenBank, an online searchable database for DNA sequences”
  • “Science Commons, a non-profit project at MIT to make research more efficient via the Web, such as enabling easy online ordering of lab materials referenced in journal articles”;
  • “Online open-access (and free) journals like Public Library of Science”
  • “Open-source software that can often be downloaded free off Web sites”

Sure the article gets a few things a little mixed up. For example, software can be free even if it is not open source. And not all open access journals are the same. But the article is overall very good and has some of my favorite Open Science advocates in it like Cameron Neylon and Jean-Claude Bradley.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Open Science Highlight — JoVE: Journal of Visual Experiments

I am starting to browse around at JoVE (the Journal of Visualized Experiments).  This is an open journal dedicated to publishing biological research in a visual format.  It is pretty cool.  Some good videos include ones by Jared Ledbetter’s group on studying microbes inside termites (see Layers of Symbiosis – Visualizing the Termite Hindgut Microbial Community
and Extracting DNA from the Gut Microbes of the Termite (Zootermopsis nevadensis)) for example.  Others of interest to this blog include one by Ed Delong’s group on Large-Scale Screens of Metagenomic Libraries. 
Anyway – JoVE is definitely worth checking out … visual presentations are probably the way of the future …
In addition to experiments, JoVE also has some interviews.  For example, I am embedding a nice video from JoVE with a talk by Ed Delong on microbial communities (Microbial communities in nature and laboratory – interview (Video Protocol).   To view the embedded video click the play button below.

http://www.jove.com/index/embed.stp?ID=202

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

A million minds getting together can be confusing but might end up being really cool

Their is a possibly interesting paper in Genome Biology by Barend Mons et al: Calling on a million minds for community annotation in WikiProteins. I say possibly because the paper itself is quite confusing to me but the overall goal seems to be a cool concept. This group has created and is encouraging the use of “WikiProteins” a community annotation system for “community knowledge.” Sounds a bit fuzzy? Well, reading the paper does not completely help. For example here is the abstract

WikiProteins enables community annotation in a Wiki-based system. Extracts of major data sources have been fused into an editable environment that links out to the original sources. Data from community edits create automatic copies of the original data. Semantic technology captures concepts co-occurring in one sentence and thus potential factual statements. In addition, indirect associations between concepts have been calculated. We call on a ‘million minds’ to annotate a ‘million concepts’ and to collect facts from the literature with the reward of collaborative knowledge discovery. The system is available for beta testing at http://www.wikiprofessional.org webcite.

I got really lost reading this I confess. But I moved on since the overall concept seemed quite intriguing, even if I did not get it completely. But it did not get much clearer further on. For example consider their description of a “knowlet”

The future outlook to integrate data mining (for instance gene co-expression data) with literature mining, as formulated in the review by Jensen et al. [2], is at the core of what we aim for at the text mining/data mining interface. To support the capturing of qualitative as well as quantitative data of different natures into a light, flexible, and dynamic ontology format, we have developed a software component called Knowlets™. The Knowlets combine multiple attributes and values for relationships between concepts.

Scientific publications contain many re-iterations of factual statements. The Knowlet records relationships between two concepts only once. The attributes and values of the relationships change based on multiple instances of factual statements (the F parameter), increasing co-occurrence (the C parameter) or associations (The A parameter). This approach results in a minimal growth of the ‘concept space’ as compared to the text space (Figure 1).

OK … I got lost every time I tried to read this in detail. I do think they could benefit greatly by translating their paper from the language used by people who work on text mining to a broader presentation.

But reading between the lines here, this is a new, apparently open access system to try and get community annotation for “Concepts” and for relationships among concepts in biological sciences. Those concepts could include a wide range of things, including genes, genomes, proteins, as well as more standard concepts like functions. Whatever this system is, it seems worth checking out.

I leave you with their ending:

Once widely used and augmented, this resource could become an open, yet quality assured and comprehensive, environment for collaborative reference and knowledge discovery.

Now that I can say I understand and it sounds good to me. If anyone out there has any more insight into this, please give your input.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–