Steve Koch

Any plan for Mendeley to allow adding data sets and / or figures? I.e., things citable with handles that don't have PDFs... - Steve Koch

Here's a question for you: since one person has already completed the assignment and provided a link, are you concerned about people copying? If it's not for assessment they're only cheating themselves, of course, but different teachers have different approaches to that issue. - Bill Hooker

It's a really small class, and they all know that I'm most concerned about them getting experience and learning. They know that I expect them to look at each other's work if they want to, just that they should give credit when credit is due. In the other class (Junior Lab), that worked very well. In this class, I've been struggling just to keep up with the content (new class for me) and haven't been stressing citations enough. But I can easily tell whether a student did any exploration on their own when they did the assignment, and they know that's what I'm looking for. To be less long-winded, as you pointed out, I don't care at all about catching someone "cheating," unless it's sort of an accident. If they want to cheat themselves, then I stop caring about them. - Steve Koch

Steve - you can already attach all sorts of supplementary info such as presentations, spreadsheets, and images to items, but you'd need to make the entry manually if you wanted to cite it separately. - Mr. Gunn

This is the data set for a figure I published in 2003 (PRL 91.028103). Seems just bizarre to me that this data hasn't been published for 8 years. And that now that I finally have, I can't add any link to the original article page on PRL website. - Steve Koch

You can do _that_? Cool. - Pawel Szczesny

This is my first try uploading a pptx file. It links to a Google doc PDF that shows figures. Not sure if this will be useful or whether PNG would be better. - Steve Koch

A possible solution would be to encourage people to upload graphical figures (e.g. PNG) and have a box on the figure creation form that allows also optional uploading original figure file. (B) Or, if possible, could have a preview ability for PPTX and other files, based on Zoho or Google Docs? I have no idea if that is possible, but it was pretty slick the Zoho preview on the data set I uploaded! - Steve Koch

This is a figure I made in 2002/2003 to explain the "loading rate clamp" I coded to my advisor and to possibly publish. I never published it. It probably would have made our 2003 PRL more understandable. - Steve Koch

This is the first figure our lab has added to FigShare that is new and very likely to be (formally) published soon. It's Andy Maloney's data for microtubule gliding speed on a kinesin-1 surface as he varies the concentration of deuterium or heavy-oxygen in the water. I think his data are exceptionally high-quality and I'm really proud of his work. These two plots are the culmination of a ton of work by him and Larry Herskowitz (image tracking) over the past two years (since we began working on kinesin). I'm not sure but I think there are between 100GB to 1 TB of raw image data associated with these graphs. Not a lot, but not a little data either. It's all open data and we're working on methods for sharing the data. Probably a good page to jump to is Andy's methods in his open dissertation: http://www.openwetware.org/wiki... - Steve Koch

Something else you've probably already thought of -- the Pi exchange/ADP release is a good idea, so I wonder if there are other well characterised systems which include a similar step that would be amenable to study in your setup. I got there from here: what do seeds (Lewis) and tumors (PubMed search for DDW) have in common? Rapid growth and proliferation, which requires rapid DNA synthesis, which involves the sorts of phosphotransactions we are talking about... probably bullshit but thought I'd dump it here anyway. - Bill Hooker

I've been jonesing for more data on this question! - Bill Hooker

Me too! Andy has overhauled the data acquisition system with like 8 web cams now. It's a very cool system, but because it kept crashing, we had to abandon the idea of real-time data to the web. I think he started a new experiment yesterday and it will be fun to see what happens. For what it's worth, though, my bet is still that we will not have enough precision to discern a difference between regular water and deuterium-depleted water, relative to what I expect will be large uncertainty. My gut still tells me that life would have evolved a use for deuterium, so there should be _some_ effect. I just don't think we'll be able to discern it yet. But even just replicating Lewis's 1933/1934 experiments is fun! - Steve Koch

Well, I didn't soak anything so we shall see what happens. - Andy Maloney

It may be fine, just depends on how much H is stored in seeds and how quickly it exchanges. - Steve Koch

This was very interesting, thanks for posting it. I'm curious as to where the idea of using deuterium-depleted water as a medical treatment originated, and also what condition the person was hoping to treat with it. - Caleb D. Morse

And I answered my own question. There's a lot out there about it being used to treat cancer. But, the majority of the websites are making exceptional, and apparently unsubstantiated, claims. - Caleb D. Morse

Glad you liked it, Caleb. I guess you definitely proved that me posting it publicly was beneficial to at least one person! I'm glad the person who sent me the email was up for it. As far as I can tell, the idea originated via those researchers who published articles showing cancer cell lines and tumors in mice grew more slowly in D-depleted water. Very very very limited published research, though. - Steve Koch

==Homework review== ==Osmotic Pressure / Protein-DNA== * Ratio of specific to non-specific protein-DNA binding * Kinetic scheme for protein-DNA interactions * Sidorova and Rau extension to off rate analysis ==Free Energy diagram for protein unbinding== * Change as water chemical potential decreases * Hint at force ==Polymer physics models (intro)== * DNA overstretching / polysaccharide stretching - Steve Koch

There's nothing obviously missing as far as I can tell. - Mr. Gunn

Neil's stuff is missing all over FF -- I assumed it disappeared when he deleted his account. - Bill Hooker

Bill, that is probably it. Wow. That fucking sucks. - Steve Koch

Yeah, I bet Neil didn't expect that to happen. I've never seen a "delete account" that wipes all previous activity. - Bill Hooker

Wanting to add this to FigShare later. Demonstrates that DNA overstretching is very similar to unzipping, with melt/anneal cycles. http://kochlab.org/files... File: - Steve Koch

Kudos for clever science and inventing valuable technique to answer important biological questions. Unkudos for minimizing impact by keeping other scientists from duplicating, improving, and simplifying the methods. - Steve Koch

I'd say some techniques just are difficult. I know how some techniques work and the methods are impeccable, but I just never would want to do them. I suppose this would still be similar if my machine weren't so damn complicated: my dream is to get a run of 50 or so machines produced, which would probably saturate the market for 40 years :-) - Björn Brembs

via Anthony - Steve Koch

Fantastic Steve. Keep them coming! Just getting through any fixes needed and trying to get it to the optimum before unleashing it as a beta. It would be really great to have a nicely populated dataset for people to search by then. Cheers. - science3point0

@science3point0 the site is great. For this particular figure, I think I may have broke the "has description=" parameter on the form? I used the form for editing, and I pasted in wiki code from another wiki page. I think the use of ==headings== may not be compatible with the template? It looks pretty much OK (can't access it right this second), but I suspect that it may screw up some things your template is meant to do? Obviously, I can avoid doing that, but I figured you'd want to know about a way users could cause some problems, despite the use of forms. - Steve Koch

It looked okayish to me, obviously the image links didnt work but in terms of structure, it looked okay to me. Keep trying to break it please. I'm down to one known bug to fix! - science3point0

Hey Mark -- Actually, it was a different figure that had the problem. See http://figshare.com/figures..., in the "Description" heading, the text [[Has Description is showing on the page, I think because of the wiki text I posted in the edit form. Also at the bottom there are two ]] - Steve Koch