Davis Open Science/Meeting Notes

Meeting notes for Davis Open Science:

July 6, 2011 Peeps Agenda Notes Week of Welcome Statement Jason's WoW game idea Carl's introduction for students in his department Goals March 2, 2011 Peeps Agenda Notes Carl's recent NSF workshop Symposium February 2, 2011 October 6, 2010 Wednesday, June 2nd, 2010 Wednesday, May 5th, 2010 Wednesday, April 7, 2010

July 6, 2011

Peeps

• Luke

• Jason
  

• Robin
  

• Carl
  

Agenda

• Week of welcome presentation/session

Notes

Week of Welcome Statement

Things I wish I new three years ago — Hear how fellow graduate students are making research more collaborative. Blazing new trails on how data and scientific tools are shared, and opening up our research to the world. See how to use social networking tools to increase the impact of your work. Learn approaches you won't hear about in class that will give you an edge on your research.

Jason's WoW game idea

• Some sort of game that would illustrate how collaboration can be get you ahead faster than competition

Carl's introduction for students in his department

• Mendeley
  

• Creating a science website
  

• Examples of very successful open science (polymath project)

Goals

• elect a president
  

• new members
  

• would being a campus group help recruitment?
  

• slide show we can train others to give

March 2, 2011

Peeps

• Carl

• Luke
  

• Betta
  

• Jason
  

• Robin
  

Agenda

• Planning for the graduate student symposium

Notes

Carl's recent NSF workshop

• Carl just had the first day of the NSF data management workshop today, it went pretty good but he wishes he moderated to hold people to time

• Speakers: Jonathan E., Marcel, CDL folks

• It was aimed at Ecology (some publishers are requiring data sharing, and the funding)
  

• Society journals have been successful cause they are locked by making profit from the journals
  

• The journals didn't have much tech to handle data management
  

• Supplement references are not indexed by web of science and the journal aggregators
  

• Journals typically don't have camera ready templates, even the online only ones
  

• Jim Carrey wants to teach a seminar on recording talks and screencasts with minimal effort
  

Symposium

• It is on the weekend of April 22

• Bring folks for the panel or have mostly grad students, or both?
  

• Luke will ask Cass how long the session will be.
  

• Should be interesting to a general grad student audience
  

• Students contention points: someone will misrepresent my data, someone will scoop my conclusions
  

• The stage: state of science as we know it, show studies that show the current way doesn't work well, then show the altenatives
  

• When is too much? save it all, or not? how detailed does it need to be?
  

• Share all computer code?
  

• My field is big and messy, it doesn't fit into a mold of data, what is the solution for me
  

• Why are we doing all this (science)?
  

• example: sf put police records on the web....people make cool apps for it
  

• business as usual science then funders changing the game, and publishers the game
  

• let audience participate: submit questions via card or give them microphone
  

• Tricia Cruise, Phoebe
  

• Who are the people we want?
  

• What are we asking from the panelists? We need a clear idea before approaching them
  

• Many ways that you may not like this issue
  

• Go in with a particular vision for what you want each panelist to say
  

• General concepts about data sharing not the nitty gritty details
  

• Paint the picture about sharing common data on repositories
  

• Goal: engaged audience that can ask questions, we need folks that can answer them, we need some people in the know on the panel
  

• Moderator seeds questions
  

• We need a good intro to paint the picture and tell about each of the speakers (briefly)
  

• Then field questions from the audience for the panelists...sorta like the presidential debates, the panelists will have limited time to answer and we moderate them
  

• We rehearse this to make sure we are good moderators
  

• Jason will send out an email to openscience asking for suggestions for the positions
  

• Luke will ask Cass about the date we will know we got it.
  

February 2, 2011

February 2nd, 2011 Open Science

next thing: on campus even with UC Digital Libraries
David Dryad
http://www.cdlib.org/services/uc3/
http://merritt.cdlib.org/

In attendence: Luke, Carl, Jason, Phoebe
New guests: Robin (Plant Pathology post-doc), George Perry (local Davis-ite)

The future of data, how science archives data, doi’s for the paper, but also a doi for the data. Learning about the UCDL and how to use them and what they offer.

Carl sent an email to the group which polled people about their feelings regarding open access.

Comments about what fields

Science Online: conference Carl attended. Originally about how to communicating science to the public. Has since evolved to digesting scientific results and talking about them. Example of Arsenic paper in Science because it got a much better peer review on the internet than it did by the formal review channels.

Carl talking about how his notebook is purely electronic — he doesn't do any transcription from paper to a compute.

Technology limiting factor in many cases since transcription is a pain and error prone.

Robin asked what our primary goals are?
Jason: Putting on talks that are relevant to the group members: Mendeley, Open Access week, Jonathen Eisen visiter (founder of PLoS), making lectures available online through ItunesU.

Possibility of meeting location change:

Phoebe rolls in at 6:15pm brings up the idea of collaboration between Open Science and UC Davis Open Science. Nothing like a law to make people act to make their data open.

Submitting an abstract to IGS, topic ideas:

• NSF Data Management topic. panel members: librarian, grad students faculty, will the CDL satisfy the NSF requirements? We should talk to the Office of Research, and the library, and the NSF. Jim Carrey (entomology) works CDL and may know the whys and wherefores about the CDL and the NSF Data management plans. Why the NSF is making you do this?
  

• Broader Topic: Open Science?
  

• Learning a tool/skill. Maybe a workshopy type thing?

Phoebe: library can offer: space, can get in touch with CDL, nobody is an expert on the NSF Data management plan but there might be somebody close to the boundary of the library and the NSF, if so perhaps they could dig in to

Office of Research: how much comes to the UC Davis from NSF? or the UC's as a whole?

email to list: Google Doc, NSF Data management plan. 250 word abstract due 2/9/2011

making our group official? Do campus groups get money? How many members are needed? What are the details?

October 6, 2010

Agenda

Introduction about the group
who we are
what we do
Introduction from the people
Open Access week
what’s going on
how can we help
videoing the talks
ITunesU — encourage profs and yourselves

Attendees (excuse name mispells)

Jason - Mech Engr
Betta
Name?? - from Sri Lanka
Carl - pop bio
Charlie - math?
Bonnie - Nutr Bio
Zoltan - from Hungary
Arpad - from Hungary
Paul - Emergency medical Man, likes going to lectures at UCD
Notes

last year more articles were published open access than not
PloS requires you to agree to provide your data
NSF has started reqs for data management

ITunesU >> convince your profs to have their lectures online!!! talk to Jason if interested for yourself or professor.

Funders are pushing for more openness (NIH...all should be open access within 6 months, NSF database)
1. Help communicate ideas about open science (campus dialogue)
2. Tools (paying for open access journals, software)
3. Activism (organizing to help make change happen with regards to open science)

What is Open Science???
- Open access: most is subscription based (read for free? reuse it for free?)
- Open Data: sharing raw data
- Sharing educational material so people can reuse
- Open source software: sharing for reuse
- Crowd funding for science (public can directly donate for science): fundscience, eurekafund
- Open law databases
- Patents and ownership of ideas (patents of pharmaceuticals, seeds, genes, technology, etc)

Ownership of information is a conflict, how do we reconcile sharing our data? what if we are scooped?
This is very related to the current reward system for scientists. Publications are our money. Can we value data equal to publications?
The incentive system needs to change...My data has been downloaded n times. We need stats beyond counting publications.

Open Access Week
4 talks Oct 18-22
Jonathan WIllibanks: Creative Commons:
Jonathan Eisen: PLoS Biology
California Digital Library

We can help by advertising!! Let’s let all the departments, grad groups, etc!
We need fliers for the event to be made and posted. We also need some handouts for the talks so people learn about our group.
Want to video a talk?? Talk to Jason

Jonathan Eisen’s grant: environmental microbes, have to show how to do the research in an open collaborative level, hoping he will generate the next generation of tools.

The Craft Center has uc copyright clauses.

Most university patent departments don’t actually make any money.

You have to have IP protection to get funding, there aren’t many other options.

Forum type conversation after the Open Access Week talks.
Many people don’t know what the policies are at UC Davis for Open science issues.
Teach-ins on copyright laws.
Invite speakers and have discussion at a more formal venue.
Debates: find the controversy and get to opposing people in the room for us to watch.

Can help prevent fabrication of data and no one will die with their datasets. old scientists should be the first required to make their data available before they die!

If you put your data out their, then the process of getting grants should be easier.

Some journals don’t consider data as an intellectual contribution.

Author order: just a technological hurdle. there could surely be rankings or counts in a database of authorship rank.

No one wanted to put their data on GenBank, but it was required to and now it wouldn’t be any different.

Does EPA have any Open reqs?

Can Google be one of the entities that can help open science? They could help in funding, but they want access to search your data. Science is hidden from google just like us. Crowd funding (donate and get early access to data/papers from the study, participating in exclusive blog conversation)

Ways to channel people to the crowd funding sites. Google can provide lots of traffics. Kickstarter based on social networking more than from search engine. Google ads for donating to research topics.

Wednesday, June 2nd, 2010

Attendance: Susanne Rockwell, Jason Moore, Luke Peterson, Thomas Johnston

Susanne Rockwell came to speak about UC Davis's initiative in open courseware.

• She has about 20 UC Davis courses on ITunesU
  

• Tim Morton (English Prof) has about a half million downloads for his course
  

• Victoria Cross in Psychology has about 250,000 downloads
  

• Susanne talked to the teaching resources center but they weren't ready to take on Open Courseware in their agenda
  

• Some of the reasons profs don't want to do open courseware:
  

• African American studies prof said that classroom discussions were too personal to be publically available
  

• Psychology prof said that he doesn't want to give away good ideas that is shared in class
  

• Some only want internal pod casts due to ownership issues
  

• They feel like they will be loosing their intellectual property
  

• the profs may be misusing copyrighted material in their classes (music, movies, etc) and exposing their class to the internet could get them in trouble
  

• LAWR prof said that they would have to change they way the taught because you couldn't use material that is copyrighted (they already use a lot)
  

• A prof in animal science was worried about animal rights people giving him a hard time
  

• If the classes are on the internet then it is out of context and you can't explain certain things that are said or shown in the class
  

• It is hard to see powerpoint in the video
  

• If you only record audio you may miss stuff too (but this works well for the Tim Morton)
  

• students will stop coming to class if we put it on the web
  

• Apple's role with ITunesU. They own Itunes. They host the content. The University owns the material but ITunes/Apple hosts it. The Regent's own the copyright to the material. The professor owns the IP within, but recording is owned by the University.
  

• UC Davis has about 60 to 80 thousand downloads a month on our ItunesU
  

• There are only 16 profs that make their classes available on the web
  

• Media Works records 25 to 30 courses a quarter already
  

• Jonathan Eisen was all about it but was worried and stopped cause he had other's IP in his talks
  

• Jonathan got some funding to record his course
  

• The whole MIT faculty made a commitment to post all of their courses
  

• Folks at Berkeley did more of a gorilla movement and had some seed money
  

• UC Davis does it without any money
  

• Charlie Turner and Susanne Rockwell are the only two people that work on getting courses online
  

• We put material on youtube too, including a couple of courses
  

• ItunesU seems more tailored to classes and is focused to a specific crowd. Youtube is so general it is hard for the courses to find the right group. You have to download the Itunes software to see Itunes courses, but Youtube only requires a flash enabled browser
  

• The “Longtail” is a book about how the web has changed and how we are able to now reach small finite audiences
  

• UC Davis designed piece of software for profs to upload their stuff to Itunes and Youtube easily
  

• We can help Susanne by getting more profs to agree to put their classes online
  

• Berkeley had a pot of money to help things happen, they also had a cover story about an soldier in Iraq taking all their chemistry courses that gained a lot of good press
  

• Another downside: You can't get a degree from watching courses on ItunesU
  

• What is UC Davis's real purpose for doing open courses? It shows the high quality of education at UC davis, gives a good feeling and shows a commitment to spreading knowledge to the world.
  

• Knowledge for knowledge sake
  

• Tim Morton's lectures are really out there.
  

• How did MIT get the faculty to agree? Faculty leaders (academic senate) must have lead it
  

• Berkley does automatic recording (so the prof doesn't have to think about it and doesn't need to know anything about the technology)
  

• MIT has made an institutional commitment
  

• chronicle of higher education — get articles from that about other schools doing these open courses
  

• Bernt Hamnm from computer science would be interested, Tim Morton, Tor (or Victoria?) Cross (psycology), also a plant sciences person (his name is in the story that Susanne will send out)
  

• Students that listen to the podcasts have deeper conversations in office hours (according to some profs)
  

• some think students do worse, some think they do better
  

• competition among professors on who can get the most downloads could be an incentive for them to post their courses
  

• european model—giant exam at the end of the year versus american model—projects and term papers throughout the year
  

• is it our duty as a university to benefit the public?
  

• Find the faculty that really believe in teaching, they will be interested in posting their courses
  

• Target lecturers? Instead of research faculty?
  

• It shows good teaching...mostly good teachers want to do this
  

• social justice people may be into it
  

• openconsotium – people put up courses for free (need some faculty leadership to make this happen)
  

• We need to get a certain amount of profs to buy in and post their courses...then more will follow
  

• We also need some kind of incentive for profs to post their courses, a reason to do it
  

• Susanne will send us the article she wrote about Open Courseware @ UC Davis
  

• She will also send us a list of profs that are interested (we need more faculty in the open science group!)

Wednesday, May 5th, 2010

Attendance:
Darach Miller - biosomething
Yumiko Henneberry - Hydrology
Richard - alumni
Phoebe – librarian
Jason – MAE
Carl
Luke

agenda:
open access week (oct 18-25)
micheal eisen
advocacy
victoria stadden paper—reproducible research

the discussion:
uc regents don't accept GPL v3, but as students you can sorta do what you want

Open access week
Phoebe is leading open access week, she needs ideas!
spark and advocacies groups push this
international day with videos, panels
the library will do a series of events...speakers, panels, tabling
I GEN team (bio robot) will be finished. There is a davis group that could present about their open design process, parts registry.org
Synthetic biology club is starting up
Call out onto the mailing list to find people that do open work: poster presentations
Demonstration of bacteria (the bacteria will take your photograph)...
the broad mission: raise awareness of open access (broadly defined), publishing, copyright
Speakers on open access publishing: a how-to...what are our rights, what do we have to worry about, how to make things open but respect privacy of subjects of experiments. A shining example of open science/publishing that is applicable from all fields.
Linux user group talking about software stuff
Bill Broadley and Scott Beardsley know software stuff...reproducing the software setup
Jonathan Claremout...reproducible as a computational way
Duncan...bioinformatics, package comes along with package that reproduces the graphs
reproducability
panels for people for and against
good models of what other universities have done for the week
check out the website for open access

Michael Eisen's talk
he didn't like pdf as a good document format for searching and parsing
computer readable text
same language across the papers...so searching for a word gives good results
live documents...go beyond paper format, we have some much more interactivity
Duncan Templeline has the package that makes the whole document from data processing to final paper output in one package
matplotlib website is built from a scripts in a similar way, package is called sphinx
stop thinking in paper world, why can't journal papers be a video, or ineractive program
DOI: they are controlled a foundation, could cite the paper by the DOI...it should always get you to the paper
new ideas for developing an identifier for data are starting up
author's name is not a great identifier...unique identifiers for authors for tracking their papers
eisen totally rejected pre peer review. He thought post review is the way to go!
The arxiv is no longer open to anyone to publish without a sponsor
does the current peer review system work? Does it provide value?
Peer review is a filter
post review can be multiple things: review is shown, more than 2 reviewers so there are some statistics
5 reviews gives a binary system, in or out
books have editors to make sure it is ok, articles don't have this
why is the paper static...shouldn't we be able to fix it
how do you cite something that isn't static??
version tracking for content of articles....computer programmers already have this
cite specific contents of a paper instead of the whole paper
plos one allows intext commenting
Jango manual has this kind of inline commenting
nobody does the standard commenting
what if the commenting is useful for use personally?

Advocacy
copyrights are one place to start
public needs to give us more money to keep the uni alive, but we don't even give them the science back for free
the IP department at berkley doesn't bring in more money than it takes to manage the IP
publishing policy comes from the journals themselves
researchers need to talk with the publishers
policy—can our faculty demand all published material to be available publicly in 6 months (havard/mit did it)
we pay tons of money for Elsevier
the publishers have more pressure over the library than vice versa
we need research community and library to team up on the publishers to change
free viewing is not necessarily open access
E scholarship is the (UC) university's publishing mechanism, we can publish stuff here, preprints, reports, etc

Victoria Stadden's paper
goes through creative commons licenses
the creative commons licenses are discouraged for code
licensing the output of the code instead of the code itself for graphics
talks about for licenses for media, code, data, papers and recommdends licenses
patent principles for data have just been given at a conference
what's the difference in licensing the data vs the code that processes the data vs the code that produces the figure vs the code that produces the document

Wednesday, April 7, 2010

Attendance
Phoebe – librarian
bill kendrick – lugod
carl
jason
luke
mike nano/micro guy
rob physics
yumi hydrology
betta - environmental

Notes

• finishing.com....great community, great resource to find out about metal finishing, good model for a website for sharing knowledge
  

• we need a place on the web that tells us what went wrong, not what went right
  

• open notebook is an initiative to do this
  

• archive.org indexing the internet
  

• arxiv.org math and physics preprints
  

• library has been asked to fund arXiv
  

• open access week in october 18-24 put out by libraries, need some speakers for that here on the campus
  

• experience with how to present data that can't fit in the journal paper. How do we logistically present our data? Without tons of extra effort
  

• why would I want to share the data? Genome institute is an example. NIH requires to post all the genome data. It has produced more publications.
  

• What is the practical side of sharing the data?
  

• Conferences-multimedia presentation rather than paper (new forms of showing.distibuting and sharing what we do)
  

• Large data sets? How to interpret it too? Do you need special things to view it?
  

• Database to pay access to see the molecule. You have to have access...but what it you don't even though it is in the public domain
  

• Current data versus the bread and butter of each field. The wiki does a good job
  

• Textbooks repeated information have to pay for each one...open textbook projects
  

• MIT publishes their coursework online (open courseware). Can Davis profressors do this? We need to make them aware
  

• Movement to put things on Itunes? Why there, why not a more open place?
  

• Smartsite requires and UCD account? Why?
  

• Money an be made by not doing it the open way...so there is resistance to adopting these tools
  

• Publications are currency
  

• Starting to look for speakers!!
  

• Do we need a discussion space beyond the mail list? Openwetware: wiki for pages for labs...originally based out of harvard. Orginal purpose for finding other groups that do this (4 in Davis). Lab website for users to maintain it themselves. Also lab notebooks are posted and courseware.
  

• Usenet groups were amazing. John Biaz posts 6-8 hundred lines. Moderated groups are better, the spam degrades the unmoderated groups. In forums there are questions but no answers a lot of times. Needs to be control to keep out the spam
  

• Getting help from the community through mailing lists and forums. What are the advantages? What are the pitfalls? Usenet was centralized but now there isn't a central place...too many places. Do people use stackoverflow (sysadmin forum)? Stackoverflow provided more replies than traditional online forums. Gain social capital and can spend capital to get answers. More capital for better intellgient questions.
  

• Do these sites own your data? Own your questions? Sourceforge nightmare?
  

• Version specific answers to software questions. The old things don't help you with the new versions of software.
  

• Liscensing rights, giving up the rights. Most wikis are under most creative commons.
  

• What does open access mean? Can I read if for free? Can I use your figure?
  

• Difficulties in getting the data and the rights of distrubuting the data. Sourcefrogre put in but can't get it all out.
  

• Adovacy in licensing issues is a big thing we need to look into.
  

• Stuff in smartsite is copyrgithed, Campus employees work is owned by the campus. Journals own your copyright many times too! This campus is pretty pro closed copyright.
  

• Merit for open source. Rewards for publishing in big journals but not in open journals. What can we get back from publishing open?
  

• Social capital can be a form of incentive. The publish or die mentos is immovable. Everybody cares what journal it is. Science knows that people want to publish in science. They make the library pay big money for Science. But physics is the different community..arXiv has citations as social capital. Citations can carry a lot of weight.
  

• PloS public library of science is a new revolution: open access snooty journal and reject many but still be open. You charge the author rather than the reader (sliding scale depending on country etc). They are prestiguous and competitive. PloS 1 – author pays to publishing, anything that is technically qualified should be published. It doesn't have to be cutting edge or topcial. The review is simply “Is it right?” they scored by impact factors. Look at citations more. How often downloaded? How many blogs are talking about it? Article level matrics.
  

• Library doesn't get overhead money. Libraries get normal campus money.
  

• How do we measure the quality of scientific works?
  

• PloS1 not specific to fields.
  

• We should have Dr. Esien to speak about PloS.

The mailing list is openscience@ucdavis.edu on the website.

Speaker in one month: Phoebe or Jonathan

Propose talk topic.

Meeting once a month? Speaker once a month?

First wednesdy a momtn schedule speakers as they come.

Advertising for our group: bulletin boards, cal aggie, send out to mailing lists, publish to the campus news if we get good speaker, davis wiki events page, send out to researchers –mike, tabling, picnic day, GSA mail list, hook up with Lugods speakers that are sciency, every library cares about open access,

regular schedule for speakers....

speakers and gatherings for discussions