Microbes and Infant Intestinal Health – From Development to Disease Prevention
Speaker: Dr. Karen Kalanetra, Microbial Ecologist/Molecular Biologist, UC Davis Departments of Viticulture and Enology, Food Science and Technology
Wednesday, February 17, 2016
1:10PM – 2:00PM; WHNRC Conference Room 121, 430 W. Health Sciences Drive
To be filled in for any NSF grant.
———————————————————–
In order to meet the requirements of the benevolent, wise, and all knowing HR 3293, it is hereby declared in this written declaration that this National Science Foundation grant has been determined to
1) Be eminently worthy of Federal Funding
AND
2) Is without a doubt in the national interest, as indicated by having the incredibly high probability of achieving: [Insert here one or more of the following]
(A) Increased economic competitiveness in the United States;
(B) Advancement of the health and welfare of the American public;
(C) Development of an American STEM workforce that is globally competitive;
(D) Increased public scientific literacy and public engagement with science and technology in the United States;
(E) Increased partnerships between academia and industry in the United States;
(F) Support for the national defense of the United States; or
(G) Promotion of the progress of science for the United States.
Sincerely,
Your humble National Science Foundation Program officer
if you can attend, you really should …
SETH COOPER
Using Video Games To Solve Hard Problems
Feb 12th | 4-6pm | Art Annex Rm 107
Seth Cooper is an Assistant Professor in the College of Computer and Information Science at Northeastern University and a member of the Playable Innovative Technologies Lab. His research focuses on using video games to solve difficult scientific problems; he has delivered multiple TED talks on the topic. He is co-creator of the scientific discovery games Foldit and Nanocrafter and early math educational games including Refraction and Treefrog Treasure. He has also researched real-time animation for games, and has previously worked at the Center for Game Science (as Creative Director), Square Enix, Electronic Arts, Pixar Animation Studios and the UC Berkeley Space Sciences Laboratory (on BOINC, the Berkeley Open Infrastructure for Network Computing).
Rather than solving problems with a purely computational approach, combining humans and computers can provide a means for solving problems neither could solve alone. Video games provide a compelling framework for this approach: they are a natural space for problem solving and can foster the engagement necessary for people to make a contribution. Cooper will describe the challenges of mapping real-world problems onto games and ways to address these challenges. As a primary example, he will discuss Foldit, an online game about biochemistry whose players have contributed to several scientific discoveries through gameplay. He will also discuss other current problem solving game projects on DNA nanotechnology and software verification and future possibilities.
So I discovered a few days ago I had dozens of new publications in 2015. Cool right? Here is a screengrab:
And here is another
Until I realized, well, those were published years ago. WTF are they doing being listed as 2015? Clearly some glitch. And then I saw a few Tweets that pointed me to figuring out what was going on.
.
According to Google Scholar, this 2014 paper has been cited 5 times between 1999 and 2012. #timetravel @austingmeyer pic.twitter.com/87DtVQKzAS— Claus Wilke (@ClausWilke) February 2, 2016
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This one is even better. Paper from 2015, cited 29 times from 2001–2014. @austingmeyer @carolinefarrior pic.twitter.com/clITv4Nnxo— Claus Wilke (@ClausWilke) February 2, 2016
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So I responded
so @ClausWilke @austingmeyer @carolinefarrior I have whole slew of these that showed up in my pubs today pic.twitter.com/MAwCOsxhrE— Jonathan Eisen (@phylogenomics) February 2, 2016
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.@ClausWilke @austingmeyer @carolinefarrior all are papers published while ago that were switched to new publisher site & GS got confused— Jonathan Eisen (@phylogenomics) February 2, 2016
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And some discussion followed
@phylogenomics @ClausWilke @carolinefarrior I’m surprised there’s not a one liner piece of code to prevent time travel citations— Austin Meyer (@austingmeyer) February 2, 2016
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@austingmeyer It’s not that simple, actually. They can occur legitimately with preprints. @phylogenomics @carolinefarrior— Claus Wilke (@ClausWilke) February 2, 2016
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@austingmeyer E.g., most of these time-travel citations are valid, to my knowledge. @phylogenomics @carolinefarrior pic.twitter.com/oQHwuKI281— Claus Wilke (@ClausWilke) February 2, 2016
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@austingmeyer The preprint came out 10 years before the paper. @phylogenomics @carolinefarrior @ChristophAdami— Claus Wilke (@ClausWilke) February 2, 2016
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@ClausWilke @phylogenomics @carolinefarrior @ChristophAdami well the associated preprint could easily serve as the minimum date— Austin Meyer (@austingmeyer) February 2, 2016
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Fascinating. But I knew my papers were not published as preprints. And that they were published years before Google Scholar was not listing them as being published.
So – what happened? I think I now. These papers were all published in one journal – Standards in Genomic Sciences. The journal used to be published semi-independently by the Genomics Standards Consortium. Then they were transferred to / bout.
ht by / merged with Biomed Central and even the web address was forwarded to BMC where they host the archive of articles from before the transfer. Then there is a new site with articles from after the transfer.
So when I click on the articles from the Google Scholar site I get to a strange thing. The articles published before the transfer are also listed on the new site http://standardsingenomics.biomedcentral.com/.
For example – the Complete genome sequence of Sulfurospirillum deleyianum type strain (5175T) is shown here with a 2015 publication date:
Although note the Copyright 2010 little bit. Which is interesting since this paper was in fact published in 2010. And you can find it on the other site http://standardsingenomics.org with a 2010 publication data here.
And also in Pubmed and Pubmed Central.
So – even though Biomed Central says the new papers will be in the new site and the old papers will be ket in a separate site that is not what is happening.
For some reasons some of the older papers are now being listed in the new site with a new publication date. And I assume because Google Scholar scrapes from the journal sites, it found the “new” papers and has now added them to it’s clustering collection and has fed them into my publication list. And despite trying I am not sure how to fix this.
I tried to “unmerge” the new publications to see if somehow the old publications showed up. But they did not. So .. am not sure what to do here other than to send this to BMC and Google Scholar, which I will do. Ahh – the perils of automated systems …
I note – this does seem to have possibly temporarily increased my total number of citations since it seems like some of these papers are now being considered twice by Google Scholar but not sure about that. More digging.
Caroline Dean
John Innes Center, Norwich, U.K. “Epigenetic switching in seasonal timing”
2:10 – 3:00 PM, Thursday, February 4th
1005 Genome and Biological Sciences Facility
Genome Center seminar Caroline Dean.pdf
Collecting together information about the Women in Science summit that was at the California Academy of Sciences 1/28/16. I was on one of the panels and live Tweeted the event as did an amazing collection of other people.
Storifies of Tweets by Me
Some other information and write ups:
Made a storify based on a discussion about a new Slate article:
Jonathan Eisen's Lab 