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Steve Koch

Steve Koch

Experimental Biophysicist at the University of New Mexico, USA
https://accounts.google.com/Service... Zeke, a student in Junior Electr. Lab, did a great job on Anthony's assignment to discuss value of twitter for science!
https://accounts.google.com/Service... Zeke, a student in Junior Electr. Lab, did a great job on Anthony's assignment to discuss value of twitter for science!
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
that sucks! not sure how to fix it :( - Steve Koch
You can zoom and drag the screen though. And the horizontal arrows link to sub-pages - Steve Koch
The 2012-Physics-308L-Lab-2 Network - GitHub - https://github.com/steveko...
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
RT @Thescienceofant: So much fun.. RT @kvoDE: The lucky lucky people who went to @lifeandscience for #scio12 The photo (cont) http://www.twitlonger.com/show...
R Tutorial Series: R Tutorial Series: Scatterplots - http://rtutorialseries.blogspot.com/2009...
Seems excellent for me as an R beginner - 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...
R code for producing figure: https://github.com/steveko... - Steve Koch from Bookmarklet
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 from Bookmarklet
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
My mindmeister mindmap for getting started with R statistics / graphing http://www.mindmeister.com/1275974...
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....
Annotated pdmatrix for friendfeed.png
Annotated temptationtodefect figure for friendfeed.png
Whoops. Github link was truncated https://github.com/olendor... - Steve Koch
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)... more... - 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... more... - Steve Koch
A somewhat related project is Lee Worden's "Mathematics of Direct Democracy" at http://rockethub.com/project... (or, more detailed, at http://lalashan.mcmaster.ca/theobio... ) - see also https://plus.google.com/u... on link to collective action problems. - Daniel Mietchen
Rob posted some thoughts / responses on the github wiki: https://github.com/olendor... - 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...
RC Bayes Conf 0.8.png
Revolutions: How to use a Google Spreadsheet as data in R - http://blog.revolutionanalytics.com/2009...
statistics - Is there a good R API for accessing Google Docs? - Stack Overflow - http://stackoverflow.com/questio...
Advice to junior faculty who want to do get promoted doing Open Science | The OpenScience Project - http://www.openscience.org/blog...
Is that post about you? - Anthony Salvagno from Android
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... more... - 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,... more... - Dan Gezelter
Project: Mathematics of Direct Democracy | RocketHub - http://rockethub.com/project...
22 free tools for data visualization and analysis - Computerworld - http://www.computerworld.com/s...
Steve Koch Science: Quick summary ARL / DLF E-Science Institute Capstone -- Atlanta - http://stevekochscience.blogspot.com/2011...
idea at workshop: to surmount library / researcher barrier: connect with graduate students via mandatory ethics/responsible research courses
Yes. I'm working on this where I am. It's slow going. - RepoRat
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... more... - 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
that's DEFINITELY part of the plan. :) - RepoRat
AWESOME :) - Steve Koch
idea at workshop: to surmount library / researcher barrier: connect with graduate students via mandatory ethics/responsible research courses
for 4th-grader's Acer computer, needing to install OS. no experience with linux, is #ubuntu the right choice?
RT @FigShare: "Nielsen asks scientists to reinvent what they do, for the good of science and the good of society" http://t.co/Pef8UfTD
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
An idea for wealthy donors: alternative to direct research funding: fund libraries to help with e-research - http://stevekochscience.blogspot.com/2011...
Project: Beethoven's open repository of research | RocketHub, Props to Daniel Mietchen, very cool project, already $700 in crowdfunding - http://rockethub.com/project...
Project: Beethoven's open repository of research | RocketHub, Props to Daniel Mietchen, very cool project, already $700 in crowdfunding
Project: Beethoven's open repository of research | RocketHub, Props to Daniel Mietchen, very cool project, already $700 in crowdfunding
Project: Beethoven's open repository of research | RocketHub, Props to Daniel Mietchen, very cool project, already $700 in crowdfunding
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
The #SciFund Challenge, Your opportunity to crowdfund science of your own liking. Way more fun that paying taxes! - http://scifund.wordpress.com/
The #SciFund Challenge, Your opportunity to crowdfund science of your own liking. Way more fun that paying taxes!
Is This Patient Allergic to Penicillin?, May 16, 2001, Salkind et al. 285 (19): 2498 — JAMA - http://jama.ama-assn.org/content...
Andy Maloney: Back to open science! http://andymaloney.wordpress.com/
Very impressed that Andy was able to find a postdoc position where he could do OS. - Bill Hooker
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... more... - 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
@Repo that's awesome, congrats :) - Steve Koch from Android
The inevitable spread of open science - http://stevekochscience.blogspot.com/2011...
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