http://www.mindmeister.com/1397392... Link to my presentation notes from today's talk about Open Notebook Science in Junior Lab at the "Success in the Classroom" workshop
For Lab#2 in Junior lab this week, students forked my starting project and then pushed some of their own work to github. This is a network graph that I don't understand much but looks very cool, especially as far as our goal of having the students learn git and github goes.
- Steve Koch
from Bookmarklet
thanks for the link! i've been looking to get into r and i do love a good scatterplot...
- Marie
Anthony & Alex's water FTIR data compared with Seigelstein 1981. Matches well, but path length too long for longer wavelength info. - https://github.com/steveko...
Google Docs exports spreadsheet values with commas. read.csv() in R treats these as factors instead of numeric - Stack Overflow - http://stackoverflow.com/questio...
Asked my first question on stackoverflow. Got two great answers within a couple hours. I love the crowd!
- Steve Koch
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ScienceDirect - Acta Astronautica : Deuterium-free water (1H2O) in complex life-support systems of long-term space missions - http://www.sciencedirect.com/science...
Anthony found this paper and so far it seems excellent. First, I find it fascinating that isotopic fractionation in space-station water regeneration systems is a health issue to deal with. Second, it seems to be a good review of background research, especially of some documents which appear to be in Russsian.
- Steve Koch
from Bookmarklet
Rob Olendorf has begun some calculations to frame "open" versus "closed" science in game theory context. Even the basic analysis, considering "defect" versus "tit for tat" strategies gives some illumination on the landscape for open science incentives. He and I have decided to do the work as "open science," hosted on github....
This presumes fixed strategies and rational decisions I presume? So there are also marketing effects in here as well? Not just what are the percentage of players in each camp but the perceived percentage?
- Cameron Neylon
Important theory... now many tend to think that Closed Science only takes advantage of Open Science... game theory can provide some (theoretical) evidence for that.... interesting!
- Egon Willighagen
Open science has many "players". Do the arguments hold if I am Player 1 and the crowd is Player 2?
- Matthew Todd
If you haven't already, you should check the literature on game theory and collective action problems (e.g., http://scholar.google.com/scholar... ) Open science is an example of a collective action problem.
- Michael Nielsen
@Michael, I haven't read any background yet. Rob has, I'm sure, as he used this in his Ph.D. research in evolutionary biology (experiment + modeling/theory). I'm hoping I can get his attention / contribution on this thread soon! I don't have any background in game theory. But, as far as I understand, the analysis Rob's done so far is the most basic first step, and tit for tat (TFT)...
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- Steve Koch
@Mat I am not sure. I'm going to see if I can get Rob to chime in here!
- Steve Koch
@Cameron, I think this starting point is fixed strategies, either "defect" or "tit for tat." Like I said in one legend, I can't remember what "temptation to defect" means exactly. I don't think perception is modeled in this basic starting point. I sent an email to Rob urging him to chime in on this thread, so I hope he can!
- Steve Koch
Good to see this being tackled in a more formal way, but sure, the simple 2x2 matrix is only the first step. For instance, collaboration can well occur behind closed doors.
- Daniel Mietchen
Side issue: Wouldn't something like Octave or R be a better fit to an open project than MATLAB?
- Daniel Mietchen
Totally agree open coding platform would be better. Right now there's not much code at all, since it's analytical that Rob did. (Rob, can you post snapshot images of your calculations, if any?) Since right now it's just plotting, R would be good. (I added the text to his images via powerpoint, just for convenience.) I am tempted later tonight to make the pots in R. A further aside: I...
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- Steve Koch
Started a github project for R code and graphs for Anthony and Alex's deuterium-depletion studies. Learned a bit about binomial confidence intervals, made new graph https://github.com/steveko...
Can u include any more info for ur dossier? I can give you the analytics for my notebook.
- Anthony Salvagno
from Android
After reading this, I'll ad a section to my CV: 'peer-reviewed methods' right after 'peer-reviewed original research'. This new section will also have download stats to our software at http://buridan.sourceforge.net (as soon as our paper describing that package is out).
- Björn Brembs
"Use as many metrics to back up your contributions as you can." Anyone have metrics they'd want to help make their open science case that they can't easily get to now?
- Heather Piwowar
@Ant: Yes! Dan was extraordinarily helpful with advice and letter for me. He's one of many generous, helpful, and successful open scientists out there & why I know regardless of my own tenure decision, open science contributions will be rewarded. Fundamentally, it makes for much, much higher impact science and since most scientists want that, the reward system will come around.
- Steve Koch
@Heather the system you've been working on is great! Every tool that is developed in the coming years needs metrics. As Nielsen points out in his book, many of the most successful endeavors (such as the Mathworks competition and fold.it) provide instant feedback and scoring. Some very important features of those successes are (1) numerical score, (2) instant scoring, and (3) EASY...
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- Steve Koch
Steve, very useful, thanks. Nope, total-Impact doesn't have any relative metrics yet, we're trying to figure out the best way to do it...
- Heather Piwowar
The post was indeed about Steve. From my own tenure documents, providing metrics on open source software like OpenMD and Jmol was fairly easy - downloads statistics and lists of other groups actively using the software for their own research was helpful. I think finding convincing metrics for other scientific contributions is much harder, particularly for Wikipedia contributions,...
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- Dan Gezelter
Not sure that ethics would be the right edge to link researchers with librarians. Data management would seem more natural to me.
- Daniel Mietchen
Agree with Daniel - I am working with the library to build a 'information literacy' content for the medical students that opt into doing research for a semester or year.
- Kubke
Although having some courses from sociology and philosophy departments on ethics and responsible conduct could be bloody interesting!
- Kubke
Data management has several points of contact with ethics: personally-identifiable information and other human-subjects issues (which leads directly into discussions of data security), data ownership, open data, fraud avoidance, appropriate crediting...
- RepoRat
And currently, at least in the few example US universities at our working table, ethics and responsible research training courses are currently linked. Many training grants (NIH, NSF) require these courses and currently (in my experience), the courses are ad-hoc and not enthusiastically designed. So, depending on institution, it's a ripe opportunity for connecting library with graduate...
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- Steve Koch
Based on my experience with undergraduate laboratory teaching, I think that undergrad labs are a fantastic opportunity for bridging the research / library gap as far as "e-research" goes.
- Steve Koch
I agree with that as well, no surprise. :) Got a one-credit "basic data management" course on the slate for this summer. Gonna be spending a LOT of time flacking it this spring.
- RepoRat
@Repo: One idea at our table (maybe you already do this): require the students to bring data from their lab to the course and do hands-on data management. Whatever the result should be educational for all. E.g., if the student's PI says, "no you can't take the data it's mine," that's a good springboard for discussion. Or if they bring a laptop with the sole copy of data, another lesson. Etc.
- Steve Koch
RT @EvoMRI: Wouldn't it be possible to put the Wordpress installation into a GitHub repository and have each post, comment,... re: http://t.co/ouklJwZ3
Project: Beethoven's open repository of research | RocketHub, Props to Daniel Mietchen, very cool project, already $700 in crowdfunding - http://rockethub.com/project...
I fueled the project with $20...I was tempted to waive the gift, but think it will be pretty cool to receive the postcard from Daniel wherever he is when he receives the donation.
- Steve Koch
I think big factors are Andy's commitment to open science and his new PI's commitment to making an impact in science and medicine. I met Hugh Smyth a few times when he was at UNM and only detected awesomeness, both in his research and in his mentoring and concern for students. Openness is probably going to be more challenging for them, though. One reason is their research is much more...
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- Steve Koch
I can't do the math, but I love the metaphor!
- Bill Hooker
Every student we put out there tilts the scales just a little bit. I've noticed this in my own teaching -- one of my very first students spearheaded a library OA mandate in his first professional job! I almost cried when I realized I'd taught him, I was so proud -- and I'm not surprised you're starting to notice it too.
- RepoRat
"I read Nielsen's new book cover to cover on my flights to / from an Open Access Week event in Tucson this week and I give it my strongest recommendation for a pleasurable read about a crucial topic. I am a scientist and my students and I practice open science as much as possible--open notebook science, open protocols, open data, open proposals, etc. I have also seen the author, Michael Nielsen speak a couple times, and I have read many of his blog posts. So, before reading this book I didn't necessarily expect to learn much or certainly to be further convinced of the possibility of transforming science in this new era. From the moment I started reading, though, I was captivated. Many of the stories were not new to me (such as Galaxy Zoo or the polymath project), but I hadn't heard them in such detail before and I enjoyed learning a lot more about those successful crowd- or citizen-science projects. There were also many success and failure stories in open or collaborative science that...
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- Steve Koch
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