Thursday, February 11, 2016

Simple solution: Template text for "National Interest" aspect of NSF Grants

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


Saturday, February 06, 2016

A very strange & annoying Google Scholar / Biomed Central "glitch" #GamingMetrics

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.

.





So I responded


And some discussion followed





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.




Saturday, January 30, 2016

Thursday, January 14, 2016

#YAMMM Alert: NGS Data Analysis & Informatics (Yet Another Mostly Male Meeting)




Just got this email:

Dear Jonathan, 

I hope this email finds you well. I came across your profile while doing some research on the NGS Data Analysis field and I would like to invite you and your team to the “NGS Data Analysis and Informatics Conference, 2016” which will be held on the 18th and 19th of February in San Diego, USA which I hope would be of your interest. I am glad to inform one of the conference sponsors (Illumina, Seven Bridges Genomics, and Molecular Health) has helped arrange a complimentary VIP pass for you. We have limited passes which are being offered for you and some other experts in US. 

We are holding these sponsored pass until the end of this week or till these passes are taken, whichever is the earliest. Request you to kindly confirm your participation at the earliest by replying to this email. Attached is the VIP pass.
Our conference link- http://www.mnmconferences.com/ngs-data-analysis-informatics-congress-usa.html 

I would be grateful if you can share the information with your colleagues if you are not the right person to contact. Let me know if you need any further information. 

Kind Regards, Mahvish Anwar Delegate Executive- Markets and Markets Conferences

So, I checked out the meeting and the gender ratio of speakers.  Not good:
4 and 16 were counted at NGS Data Analysis #NGS. Learn more at GenderAvenger Tally




No thanks, not interested in attending, even for free, a YAMMM (Yet Another Mostly Male Meeting).

Friday, January 01, 2016

Notes from Searching for Life meeting Dec 2015 #NewLife15

I helped organize this meeting that happened Dec 16-17 in Pacifica, CA. It was mainly organized by people from DOE-JGI and Global Viral. Officially titled "Exploring Diversity of Life."