Hoping to meet with her next week to make plans for building a relationship between library and our lab in terms of conducting open science. Hopefully I'll leave updates on this thread. - Steve Koch

win!! - Stephanie•CogSciLibrarian

Fabulous !! - Graham Steel

Had the meeting a couple hours ago. Went OK, but UNM is not as far along as I'd hoped. So, currently our lab can use the dSpace IR for our preprints and perhaps zip files of data (a good thing and we'll do it), but dreams of hosting data not a reality yet. Good news is that she told me her Associate Dean, Johann van Reenen is leading a faculty search for two new slots, both of which will be working on data curation. Apparently many of the candidates have degrees in sciences (e.g. bionformatics), so that's very interesting. So, I'll contact Dr. van Reenen and talk with him. Probably nothing will happen till later in the fall when there's new faculty to speak to. - Steve Koch

Thanks for the update, Steve. - Mr. Gunn

I met van Reenen at the IEEE eScience conference I attended - need guy and it would definitely be a good idea to touch base with him. Those job descriptions are very cool, but I'm not sure if our workforce is up for them yet... - Christina Pikas

Yeah I understand it's going to take time. Overall, it's still very good to have made that connection, and the upcoming van Reenen (I sent him an email). Amazing that I can get this kind of advice and feedback so quickly from you -- FriendFeed still rocks! - Steve Koch

Met with Johann van Reenen today to talk about data curation. Overall quick comments: I am very optimistic about our partnership with the library! He's got the UNM's library on a very good track and is leading dramatic changes. There is a new hire coming in the fall, with whom we're going to work on our open data and even ONS. Johann feels like our lab is the perfect lab for the new hire to work with in furthering data curation projects at UNM. It seems like we have the necessary ingredients of money, people, infrastructure, and desire for open science to make some good progress. - Steve Koch

but I can't like this again :) - excellent! - Christina Pikas

What Christina said. I'm gonna go like the other post, because I can't like this one again. Need a "+1" button for when things on FF keep getting better! - Bill Hooker

Just only met him today and am not well-informed. My impression, though is that he's been working hard for fifteen years here at UNM to transform the library for the future. Looks like he's fought and won a bunch of battles, and the library is poised to be essential for us going forward. Like I said, based on limited info and gut instinct but I think UNM and my lab are lucky. - Steve Koch from Android

Met with Johann and the new assistant professor for data curation at UNM, Rob Olendorf, yesterday. It was a great meeting. Johann kicks ass, and Rob seems like the perfect person to work with on our open data projects. Rob has a background in molecular biology, too, so he easily understands our science. We're going to start pretty much right away with a test data curation project. The test case will probably be a set of Andy's experiments. The raw data are a series of microscope images, such as seen here http://www.youtube.com/watch... - Steve Koch

The thinking is we'll start small, with just one set of conditions. Then Rob will work with Andy to figure out how the UNM library can permanently host the following: the raw data along with meta data describing the raw data; possibly some means for viewing the raw data; our software for processing the raw data; the processed data, x&y position versus time for all the microtubules identified; the software for processing the position versus time data; speed versus time data; software for processing speed versus time data; final data that is presented in peer-reviewed publication. - Steve Koch

That's just sort of my understanding. We'll have to see how things play out as Rob works with Andy and me on this project. - Steve Koch

Oh, also we'll try to figure out how to archive Andy's open notebook on OWW. Johann (I think) mentioned the Memento project as potentially useful for that http://www.mementoweb.org/ - Steve Koch

I think Johann also mentioned use of DataCite http://www.datacite.org/ Rob mentioned that it would be great to be able to link to each of the images individually by DOI. However, that's probably not do-able in this first go-round, and instead the entire data set, or maybe big chunks will get DOI. - Steve Koch

Rob visited our lab today for 2 hours and met with Andy and me to discuss our first data curation test project. I think the meeting went really well. Rob's background in molecular genetics is very useful I think and he understands our data and workflow very well. We showed rob how Andy collects and analyzes data, from start to finish for one chunk of data. This chunk of data was a single sample, gliding motility assay in whole casein. Andy took data for about 30 minutes, 9000 images. There are three software applications that he uses (written in LabVIEW) to ultimately produce 15 publishable data points (average speed versus time) as part of one figure in the upcoming paper. - Steve Koch

We collected all this data and put them into a folder for Rob to start fiddling with to see how to best archive things. This folder is here: http://kochlab.org/files... - Steve Koch

In the processed data folders in this directory, it points to license and readme files. Rob will also look at these readme files to see where the software is and how to best archive it http://kochlab.org/files... - Steve Koch

Another component that's important is Andy's lab notebook. Use of the wayback machine may be useful here. For example, here is Andy's description of the objective heater he built for these assays: http://openwetware.org/wiki... - Steve Koch

So, there's a lot of work we need to do to. In terms of making sure we've linked all of the lab notebook entries, and also in terms of creating some new software that will turn our binary *.ini files into more readable text files which describe the software settings. I'm also going to introduce Rob to my contact at National Instruments to see if they can have discussions about how to deal with the issue that LabVIEW is a proprietary and moderately expensive platform. - Steve Koch

We were hopeful that the Wayback Machine would be of some help for archiving but it completely failed. That's one reason we spent so much time working on code to archive. http://onsarchive.wikispaces.com/ Maybe some of that can be useful - let us know. - Jean-Claude Bradley

Thanks, Jean-Claude. I had missed your bad experience with Wayback. I have previously introduced Rob to your work, and I'll send him that specific link. Please keep telling me when I'm repeating your mistakes or ignoring other good ideas :) Thank you! - Steve Koch

I don't consider anything a "mistake" - just providing feedback so people can make more informed decisions. Because discussions are so ephemeral on FF and related platforms I don't mind repeating myself if appropriate - but maybe some people do mind :) - Jean-Claude Bradley