Steve Koch

Bummer, Steve. No apology needed imo -- everyone has a mis-step now and then, especially with deadlines pressing, but few are willing to let the whole world learn from their mistakes in detail. - Bill Hooker

As promised here is the full Project Description, now on SlideShare: http://www.slideshare.net/skoch3... Thank you everyone for the support! - Steve Koch

Hi Steve: It is possible. Public/invite only group has approved "members" who can access pdfs, and unlimited followers who can see what pdfs are added and participate in the discussion forum. This is how I configure most of my domain-specific research groups. Public/open groups can't share the pdf but have unlimited members. - Carl Boettiger

Thanks, Carl, I will try that out. - Steve Koch

The actual files only sync via private groups still, but as Carl said, you can have invite only public groups that can have links which resolve to documents. - Mr. Gunn

Pranav took overstretch data sets using 0.5x popping buffer with regular H2O and also making 0.5x popping buffer by adding D2O to 1x popping buffer. The data sets are in * H2OThu, July 14, 2011 01:37:10 PM Data File Path \\Controller\users\rathi.pranav\Desktop\110714\0478.dat Header File Path\\Controller\users\rathi.pranav\Desktop\110714\0478.ini OVERSTRETCHING SAMPLE H2O;.002 * D2OThu, July 14, 2011 02:12:25 PM Data File Path \\Controller\users\rathi.pranav\Desktop\110714\0479.dat Header File Path\\Controller\users\rathi.pranav\Desktop\110714\0479.ini OVERSTRETCHING SAMPLE D2O;.002 Images of converted (preliminary calibration, no offset, etc.) can be found here:http://kochlab.org/files... Initially I went through and picked these data sets by eye, not paying attention to the overall force difference between overstretch, but just looking for things without sticking, breaking, and reasonably "flat"... - Steve Koch

Pranav took overstretch data sets using 0.5x popping buffer with regular H2O and also making 0.5x popping buffer by adding D2O to 1x popping buffer. The data sets are in * H2OThu, July 14, 2011 01:37:10 PM Data File Path \\Controller\users\rathi.pranav\Desktop\110714\0478.dat Header File Path\\Controller\users\rathi.pranav\Desktop\110714\0478.ini OVERSTRETCHING SAMPLE H2O;.002 * D2OThu, July 14, 2011 02:12:25 PM Data File Path \\Controller\users\rathi.pranav\Desktop\110714\0479.dat Header File Path\\Controller\users\rathi.pranav\Desktop\110714\0479.ini OVERSTRETCHING SAMPLE D2O;.002 Images of converted (preliminary calibration, no offset, etc.) can be found here:http://kochlab.org/files... Initially I went through and picked these data sets by eye, not paying attention to the overall force difference between overstretch, but just looking for things without sticking, breaking, and reasonably "flat"... - Steve Koch

via Antony Williams' blog - Steve Koch

via mindmeister blog - Steve Koch

Compared a simulation of the unzipping sequence Anthony created with the unzipping data that Pranav obtained last week. See the graph below, the red is the optical tweezers data, the black is the simulation. The simulation is very basic and doesn't allow for extra springiness of OT or the dsDNA anchor. But I would say clearly that Pranav unzipped the sequence that Anthony was trying to create. So, this leaves the mystery of why so few of the tethers unzip like this. Most of them (Pranav says about 30%) overstretch. about 3% of them unzipped, and the rest, I'm not sure, I think either broke or didn't do anything besides stretch. Details: * Data set:http://kochlab.org/files... 418, segment 15. unfortunately, for now, this is just the binary file, and the data need to be converted (and saved). Pranav converted these data, but the data set is not saved in a sensible form. Easily obtained upon request, of course. I can't get... - Steve Koch

"Of course, the real solution (other than for private copy editing) is not to use double-spacing at all. Universities, in particular, have no excuse for specifying double-spacing in submitted dissertations: LaTeX is a typesetting system, not a typewriter-substitute, and can (properly used) make single-spaced text even more easily readable than double-spaced typewritten text. If you have any influence on your university’s system (for example, through your dissertation supervisor), it may be worth attempting to get the rules changed (at least to permit a “well-designed book” format)." - Steve Koch

"statistics,polymer,isotope,antibiotic,transistor,laser,genome" - Steve Koch

Via Carl Boettiger - Steve Koch

2011 June 8 3:30 pm Today PCR with Priyanka. We based off Anthony's last success, but with lots of changes. Don't expect it to work with so many changes, but good practice. Recipe and program are below. Notable changes 1. 100 microliter volume instead of 50 2. OneTaq buffer 5x instead of 10x 3. Used 11 microliters of dNTPs instead of 8.4 4. We mixed taq into the master mix as last step, and then added to the tubes, which had their respective primers already added (5 microliters) Started the program, it will take about 5 hours and sit at 4C overnight. https://spreadsheets2.google.com/spreads... - Steve Koch

2011 June 8 3:30 pm Today PCR with Priyanka. We based off Anthony's last success, but with lots of changes. Don't expect it to work with so many changes, but good practice. Recipe and program are below. Notable changes 1. 100 microliter volume instead of 50 2. OneTaq buffer 5x instead of 10x 3. Used 11 microliters of dNTPs instead of 8.4 4. We mixed taq into the master mix as last step, and then added to the tubes, which had their respective primers already added (5 microliters) Started the program, it will take about 5 hours and sit at 4C overnight. - Steve Koch

Making tethers with Pranav & Priyanka * New BGB Weighed out in a boat 196 mg of Blotting Grade Blotter Added 19.6 mL of 1x Popping buffer Sterile filtered into 50 mL falcon tube. This made "2x BGB," approx 10 mg / mL BGB, assuming not a lot of protein stuck to the filter Made 1x BGB by adding 750 ul of popping buffer to 750 ul of 2x BGB. Mixed by aspiration * New Beads Took 100 ul of stock beads CP01F Lot 8892 Actual 196 mg, add 19 ml 1x Pop Diluted 5 ul + 45 ul 1x popping buffer. Sonicated for about 30 to 60 seconds, significant splashing. Quick spun to get off sides. * New Antidig Diluted fresh aliquot of antidig with 180 ul of cold 1x PBS * Clean glass Cleaned using just water and scrubbing, followed by water rinse about 6 times. My intuition is that this did not clean the glass well at all. The tape would not stick to the glass, way worse than I've ever seen it. Subsequently, both samples leaked. Sample may or may not Sample Antidig for about 4 minutes 5 s.v. BGB, 3x. Top sample... - Steve Koch

Excellent work making this video (Kudos to whoever did it!). This was a fun session. - Steve Koch

Love the PLoS advertising. Need to get some anti-shine for my head. - Steve Koch

Blah blah - Steve Koch

My opinion is let me know how it works b/c I want one, too! I did read one good editorial w/suggestions that included an LMS of some kind and offline capacity of some kind. The last time I looked at this (6 months ago), there was no real offline capacity which was being touted as both its best selling point and worst failure. Personally, I need some offline capability -- notepad, kindle app would be good. - Mickey Schafer

Thanks, All. @Chris, was there substantial benefit from simplification? Currently, my mom uses and old desktop computer and when the internet connection goes down, it's essentially broken, so I think she may satisfy the *everything* on the web requirement. A big thing I had in mind was that it would be much much much easier for her to use, and also make her more mobile and the 3G would be more reliable than her crappy DSL. - Steve Koch

From Andy - Steve Koch

At our "cyberinfrastructure day" yesterday, I met a colleague from the UNM library. She approached me with question about how to publish some research she had done on some aspect of library operations in her work. (Sorry I forget the details.) Her specific desires: (A) to get the information out there without waiting for peer review and (B) to publish in a form that will allow others to build on what she starts. She is also a little concerned about (C) credit, but not as much as A and B. She was thinking wikipedia when she approached me, but I thought not the best venue, since it's mostly original research that she wants to publish. A publicly editable Google Doc or just a wiki on wikispaces or other generic wiki site is an option. But I figured I'd ask library science friends on here if there's a better venue to reach a Library2.0 audience? Thanks! - Steve Koch

Exactly the kind of thing we are building Knowledgeblogs for http://knowledgeblog.org Can issue DOI's etc. Please get in touch if you might be interested in setting one up. Also check http://taverna.knowledgeblog.org and http://ontogenesis.knowledgeblog.org for examples and http://process.knowledgeblog.org for more about how we go about it - Daniel Swan

Cite: hdl.handle.net/10779//BsoBI-DNA_unbinding_forces_dna_unzipping_preliminary Description: DNA unzipping forces measured with optical tweezers. Protein-DNA binding impedes unzipping. Protein unbinding forces measured as function of force loading rate. Forces increase as osmotic stress is increased. See Koch, Shundrovsky, Jantzen, Wang Biophysical Journal 2002. See Koch & Wang Physical Review Letters 2003. - Steve Koch

x <- c(-1,1,2,-2,-1,1,2,-3,-2,-1,1,2,3,-3,-2,-1,1,2,3,-2,-1,1,2,-1,1,2) y <- c(3,3,3,2,2,2,2,1,1,1,1,1,1,-1,-1,-1,-1,-1,-1,-2,-2,-2,-2,-3,-3,-3) letters <- c("A","B","C","D","E","F","G","H","I","J","K","L","M","N","O","P","Q","R","S","T","U","V","W","X","Y","Z") # plot(x,y, type="n", axes="false") plot(x,y, type="n") text(x,y,letters) # axis(1, pos=-4) # axis(2, pos=-4) # axis(3, pos=4) # axis(4, pos=4) abline(h=seq(-3,3,1),lty=2, col="gray") abline(v=seq(-3,3,1),lty=2, col="gray") abline(h=0,v=0) text(x,y,letters) - Steve Koch

Great spot Steve, working on it today :) Thanks as always! - science3point0

Fixed I believe Steve, let me know if you have any further problems :) http://figshare.com/figures... - science3point0

I must admit that whenever I see these types of reference it does wind me up a bit. Clearly it's great to give attribution but I kind of think that references should pass some practical means of verifiability. - Dan Hagon

@Bill, I think the idea that a reference MUST be something revisitable is too constricting. It negates the value and contribution that informal communication makes to research. There's also a terrific history of such "informal" conversations being prime motivators in getting new science done and current work improved. Have a reference that refers to a publication doesn't guarantee the author's interpretation of the publication is sound anymore than interpretation following a conversation. I do agree that it is difficult for the reader, but most of the personal comm references I've seen refer to very specific points and not large-scale change makers. The large scale stuff is usually taken care of in acknowledgments b/c the scope of the help exceeds what can be usefully referenced. - Mickey Schafer

Brilliant stuff Steve. Thanks for continuing to spread the word. Lots happening on the dev side to make it an even more useful tool for you and your students. - science3point0