Eisen Lab Blog

YASSP (Yet another SPAMMY science publisher)

Just got an email from YAP (yet another publisher) recruiting articles for new journals.  These ones seem just about as SPAMMY as some of the other recent ones to come out.  Uggh.  Double uggh.  Email is posted below:

Introducing ‘Research Journal of Earth and Planetary Sciences”
Dear Colleague,
The Research Journal of Earth and Planetary Sciences (RJEPS) is a multidisciplinary peer-reviewed journal that will be published monthly by Global Research Journals    (http://www.globalresearchjournals.org/?a=journal&id=rjeps).                                    RJEPS is dedicated to increasing the depth of the subject across disciplines with the ultimate aim of expanding knowledge of the subject.
Editors and reviewers
RJEPS is seeking energetic, qualified and high profile researchers to join its editorial team as editors, subeditors or reviewers. Kindly send your resume to: rjeps.submit@globalresearchjournals.org
Call for Research Articles
RJEPS will cover all areas of the subject. The journal welcomes the submission of manuscripts that meet the general criteria of significance and scientific excellence, and will publish:
                                              
·  Original articles in basic and applied research
·  Case studies
·  Critical reviews, surveys, opinions, commentaries and essays
We invite you to submit your manuscript(s) to: rjeps.submit@globalresearchjournals.org
 for publication. Our objective is to inform authors of the decision on their manuscript(s) within four weeks of submission. Following acceptance, a paper will normally be published in the next issue. Guide to authors and other details are available on our website;  http://www.globalresearchjournals.org/?a=journal&id=rjeps&menu=guidelines     
 RJEPS is an Open Access Journal
One key request of researchers across the world is unrestricted access to research publications. Open access gives a worldwide audience larger than that of any subscription-based journal and thus increases the visibility and impact of published works. It also enhances indexing, retrieval power and eliminates the need for permissions to reproduce and distribute content. RJEPS is fully committed to the Open Access Initiative and will provide free access to all articles as soon as they are published.
                                                             
Best regards,
Otu Richard
Editorial Assistant
Research Journal of Earth and Planetary Sciences (RJEPS)
E-mail: rjeps.submit@globalresearchjournals,org
http://www.globalresearchjournals.org/?a=journal&id=rjeps
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

New paper: PLoS ONE: Accounting For Alignment Uncertainty in Phylogenomics

A new paper is out from the lab: PLoS ONE: Accounting For Alignment Uncertainty in Phylogenomics.

It describes the “Zorro” software for automated alignment masking.

Abstract:

Uncertainty in multiple sequence alignments has a large impact on phylogenetic analyses. Little has been done to evaluate the quality of individual positions in protein sequence alignments, which directly impact the accuracy of phylogenetic trees. Here we describe ZORRO, a probabilistic masking program that accounts for alignment uncertainty by assigning confidence scores to each alignment position. Using the BALIBASE database and in simulation studies, we demonstrate that masking by ZORRO significantly reduces the alignment uncertainty and improves the tree accuracy.

This work was supported by the Gordon and Betty Moore Foundation.

UC going smoke free sometime soon apparently

Just got this email:

UC Davis community members,
I am writing to share with you the attached letter 
from President Mark G. Yudofto chancellors regarding the University’s recent decision to make all campuses tobacco-free by 2014. The new policy direction will prohibit the smoking and chewing of tobacco, as well as the sale of tobacco products, and aligns with practices already in place at UC medical centers and many other universities.
As the President’s letter indicates, each campus will soon be developing plans for implementing this decision, and we will have more information about what this new policy process will entail for our community as the UC Davis plan takes shape. We will, of course, consult with a broad range of our campus community as we develop mechanisms to implement this new policy direction.
Sincerely,
John Meyer

Vice Chancellor, Administrative and Resource Management

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

EisenLab meeting. Jan, 18th 2012.

Hello all,

We will be meeting in room 5206 at the Genome center for our weekly lab meeting from 1:30 to 3:30pm.  Angus is presenting.

See you there.

Guillaume.

Draft post cleanup #19: Spam and biased spam at that

Yet another post in my “draft blog post cleanup” series.  Here is #19 from September 2011:

I am sure many others out there who blog have gotten this kind of message:

We at Onlinephdprograms.com recently came across your blog and were excited to share with you an article “15 Fictional Professors We Wish Were Real” was recently published on our blog and we hoped that you would be interested in featuring or mentioning it in one of your posts.

(http://www.onlinephdprograms.com/15-fictional-professors-we-wish-were-real/)

Either way, I hope you continue putting out great content through your blog. It has been a sincere pleasure to read.

Thanks for your time,
Liz Nutt

I assume that these posts that are written for this, and various other sites, are all about driving up Google Search ranking somehow.  So I normally avoid writing about them.  But I thought I would in this case because, well, their post annoyed me because of the 15 functional professors they wrote about, only one is female.  Really, that is the best they could do?  In three minutes of web surfing (e.g., browsing this site and this one) I have come up with a list of fictional female professors who certainly could have been included in their list.  And many are much more interesting than some they wrote about.  Here are some examples:

  • Eleanor Arroway – Jodie Foster’s character in Contact
  • Susan Calvin – character in Isaac Asimov’s I Robot series
….
But then I stopped because I was disappointed I could not find more functional female professors to add to my list.  I do think the list posted by the OnlinePhD site could certainly have had more women on it … but I never posted the post because I had a hard time coming up with a lot of examples … but now that I am trying to revive draft posts … well … I will put this out there even if it is an incomplete thought

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Draft post cleanup #18: Epernicus

Yet another post in my “draft blog post cleanup” series.  Here is #18, from July 2008.

Well, was going to write about Epernicus in 2008 as an interesting tool for networking scientists.  I still have an account there which I just updated a bit.  But I am not sure if Epernicus is being used much anymore.  I have focused a lot on a similar system: Mendeley though they have differences.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Draft post cleanup #17: Obama overqualified for application to be president

Yet another post in my “draft blog post cleanup” series.  Here is #17 from October 30, 2008.  I note – I never posted it because I tend to avoid politics here on the blog — but three+ years later I think it is OK …

Dear Mr. Obama


Thank you for your application for the position of 

President of the United States

Unfortunately we are unable to consider you for this position because you have been deemed overqualified.  
We believe that hiring people into positions for which they are overqualified can be damaging both to the person being hired and to morale of others working here at The White House.  Examples of your overqualifications include your rhetorical skills, your intelligence, the nearly limitless number of endorsements you have received from all sides of the political spetrum, your fanatical followers, the distinguished collection of advisors with which you have surrounded yourself, etc. etc.  Consider in contrast the qualifications of some of the other people who have applied for this job: poor rhetorical skills, bad taste in selecting assistants, lack of endorsements even by friends, etc etc.  Also consider the qualifications of the person who you will be replacing in this position.  

Given this, we believe that hiring you for this position is simply not wise.  Most likely you will be bored with carrying out the duties as established by the current 

President of the United States

which include mountain biking, meeting celebrities and athletes, attending dinners, and signing papers as instructed by the Vice President.  In addition, if we were to hire you into this position, it would have profound effects on the morale of other personnel currently in the White House who have tried to maintain a low qualification appearance in the face of the qualifications of the current President.  

Therefore, we are writing to ask if you would kindly reconsider your application to be 

President of the United States

and wonder if you would be interested in any of the other open positions which we have posted all of which by recent precedent require someone with more qualifications than those possessed by the current President and the other candidates. If a need arises for us to contact you in the future, we will do so and you have our continued good wishes.


Very truly yours,

The White House Staff
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Draft post cleanup #16: Science and Title IX

Yet another post in my “draft blog post cleanup” series.  Here is #16 from July 2008.

I had seen an article that surprised me: Findings – John Tierney – Science Has Become the New Frontier for Title Nine – NYTimes.com

In the article Tierney discussed how the Title IX statute which forbids discrimination based on gender in education and has been applied extensively to athletic endeavors was beginning to be applied to science.  Not sure what has become of this over the last 3+ years — if anyone knows more please post …

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Yet another SPAMMY Science publisher: Scientific and Academic Publishing

Uggh – just got this email. Seems there is yet another SPAMMY Science Publisher trying to get established. Here’s is a suggestion for all. Avoid these kinds of publishers. They probably do more harm than good … Plus if you can label their emails as SPAM to help out others. And I think posting comments like this will help since when people do google searches they may see the critiques as well as the journal sites.

Dear Jonathan A Eisen,

This is Scientific & Academic Publishing, USA. Nice to get your information from the journal PLOS Biology and also happy to pass on our regards to you from the editorial department of SAP.

We’ve finished reading the abstract of your paper Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote and will recommend it to our editors.If you are interested in our journals and want to publish it on our journals, please extend this paper and describe your latest research achievements and send it to us by our online submission system(http://www.manuscriptsystem.com). All manuscripts submitted will be considered for publication.

If this paper has been published, we also welcome you to submit other papers to us.

Welcome to visit our website at http://www.sapub.org.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Eisenlab meeting – Presentation schedule (revised as of Jan 13th)

Here is the presentation schedule for winter quarter for the Eisenlab meeting from 1:30 to 3:30 pm in room 5206 at the UC Davis genome center.

 

  • Jan 11th: Dongying
  • Jan 18th: Angus
  • Jan 25th: Melissa Whitaker
  • Feb 1st: Davis Coil
  • Feb 8th: Holly Bik
  • Feb 15th: Lizzy Wilbanks
  • Feb 22nd: Jenna Morgan Lang
  • Feb 29th: Holly Ganz
  • Mar 7th: Russell Neches + Ladan Doroud
  • Mar 14th: Undergrads
  • Mar 21st: John Zhang
  • Mar 28th: Spring break