Eisen Lab Blog

Faculty position in Population Genomics and Computational Biology at CSU Monterey Bay

JOB ANNOUNCEMENT:

Assistant Professor, Population Genetics and Computational Biology

The Biology program within the Division of Science and Environmental Policy at California State University, Monterey Bay seeks a population geneticist with strong computational biology skills to fill a tenure track assistant professor position. The applicant should be a dedicated teacher capable of successfully involving undergraduates in research. The successful candidate will work with other faculty to develop undergraduate curricula, professional outreach programs, and extramural research or programmatic funding. Additional information on the Division and the Biology program can be found at sep.csumb.edu, the university and its vision at about.csumb.edu/vision-statement, and our exceptional undergraduate research program at uroc.csumb.edu.

Continue reading “Faculty position in Population Genomics and Computational Biology at CSU Monterey Bay”

Advice needed from a future reviewer…

I found myself writing this email to some collaborators, but halfway through realized that it’d be nice to get EVERYBODY’s input. Probably, one of you is going to review my next paper, so how awesome would it be for you to just tell me what you think now, and make both of our lives easier later.

To test whether taxa vary significantly across groups of samples, we first need to filter the OTU table to get rid of OTUs that are not present in most of the samples and/or that do not vary across samples. This must happen for statistical reasons.

As far as I know, there are two ways to do this. One, is to remove OTUs that occur in fewer than 25% of the samples (25% is suggested by the QIIME folks). The other is to calculate the variance of the OTUs across samples and remove the OTUs that have a variance less than 0.00001 (0.00001 is an arbitrary number thrown out there by the phyloseq developer.)

A third option would be to apply both criteria.

My inclination would be to go with the third option, but mostly because I want to limit as much as possible the number of hypothesis tests that we do in order to avoid draconian p-value corrections.

I’m not a big fan of arbitrary thresholds, but they are so frequently required that I’ve made my peace with them. However, if someone can suggest a non-arbitrary threshold, that’d be great.

But mostly, I want to make sure that everyone agrees now on the method that we use so that I only have to do this once. Thoughts?

A year ago, I came up with a great acronym for our project – ICIS – what do I do now?

About a year ago, when we starting meeting and discussing our new project on the future of scholarly communications, we decided it would be important to have a title and if possible a brief acronym. Now – I love coming up with such project names and acronyms and think I have done a good job with such tasks in the past.  Somehow I wanted to find a cool acronym for a project on scholarly communication, and publishing, and openness, and social media and more.  And I just could not come up with anything great.  

And this was starting to get semi urgent since we had a meeting coming up and needed to make a web site and needed names and titles and such.  So the group of us involved in the project (myself, Mackenzie Smith and Mario Biagioli) started sending around ideas to each other. Among the ideas first proposed:

  • IFHA Innovating Academic Publishing Project
  • The UC Davis IFHA project on Innovating Academic Publishing” with a project acronym of IAP

But I did not like this so I started doodling:

Screenshot 2014-10-23 14.36.48

Screenshot 2014-10-23 14.35.45

So I compiled some ideas and sent around a list

  • ISP: Innovating Scholarly Publishing
  • iSP: Innovating Scholarly Publishing
  • i2SP: Innovations in Scholarly Publishing  (with the 2 being a superscript)
  • i2AP: Innovations in Academic Publishing  (with the 2 being a superscript)
  • i2SP2: Innovations in Scholarly Publishing Project  (with the 2 being a superscript)
  • i2AP2: Innovations in Academic Publishing Project  (with the 2 being a superscript)
  • IN-A-PUB: Innovating Academic Publishing
  • SP2.0: Scholarly Publishing 2.0

Other ideas circulated (some mine, some others)

  • LIAP: Lab for Innovating Scholarly Communication, pronounced LEAP?
  • Innovating Academic Communication – IACOM
  • Innovating Academic Publishing – IAPUB
  • Innovating Scholarly Publishing – ISPUB
  • Innovating Scholarly Communication – ISCOM or INSCOM
  • COMMIS: communications innovation in scholarship

And then I came up with one I loved and sent around a suggestion:

“ok here is my favorite so far – innovating communication in scholarship – ICIS (pronounced isis —)”

Other ideas circulated:

  • pubs 2.0
  • innopubs
  • scholar 2.0

But I said I still liked ICIS best and, well, it won.  Yay.  We had a project name.   And we used it for our meetings and our website: icis.ucdavis.edu.  I was so proud of this name.  It sounded nice.  It conjured up images of ISIS the Goddess.  And every time we discussed the project I could remember the struggle to come up with a name and how happy I was when it came to me.

And then the ICIS name got, well, polluted.  Or, at least, the sound of the name got polluted by the group known variously as the Islamic State of Iraq and the Levant (aka ISIL), Islamic State of Iraq and Syria (aka ISIS).  And though I would hope it would be clear that our ICIS project is not connected in any way to ISIL/ISIS.  But yet, when I mention the project name to people, I invariable get some comment.  And Alison Fish, the first post doc working on the project just told me that she also gets some murmuring when she mentions the name during talks.

So we are in the midst of our annual retreat for the project now.  We have six people working on the project – myself, Mario Biagioli, Mackenzie Smith, Allison Fish, Alessandro Delfanti, and Alexandra Lippman.  And we all liek the ICIS name but are not sure what to do now?  So – in the interest of openness and communication I proposed to everyone (and they at least seemed to agree) that it might be good to ask the broader community for input here.

So – any suggestions?  What do you recommend we do?  Should we change the name?  Change how we say it?  Should we stick to our name and pronunciation?  And ideas, thoughts, or suggestions would be welcome.

Curating a Storify About this

//storify.com/phylogenomics/should-we-rename-our-icis-project/embed?template=slideshow//storify.com/phylogenomics/should-we-rename-our-icis-project.js?template=slideshow
[View the story “Should we rename our ICIS project?” on Storify]

Microbiology Book for Kids: It’s Catching by Jennifer Gardy and Josh Holinaty

A few days ago I wrote about how I wanted to share some information about what I have found to be good childrens’ science books (based on reading books to my kids).  Well, here is another one: It’s Catching: The Infectious World of Germs and Microbes by Jennifer Gardy and Josh Holinaty.

I first became aware of Jennifer Gardy’s talents in making catchy microbe-themed kids material when she released the Youtube video “The A-Z of Epidemiology: germs from Anthrax to Zoonoses. A disturbing bedtime book for kids.” which is simply awesome. (Note – great animation by Tom Scott):

I watched this video many many many times with my kids – always resulting in painful laughter and entertainment.

I should note that I am collaborating with Jennifer on at least one project (The Kitten Microbiome) and think she is a brilliant scientist and science communicator.  But once I saw her “It’s Catching” I realized she really could have a full career as a children’s science book and video maker.  It’s Catching is both entertaining (like the video) but also educational with information on the history of microbiology and how microbes are studied.  Definitely a good one if you are looking for fun and funny science and/or microbiology themed books for kids.

  //ws-na.amazon-adsystem.com/widgets/q?ServiceVersion=20070822&OneJS=1&Operation=GetAdHtml&MarketPlace=US&source=ac&ref=tf_til&ad_type=product_link&tracking_id=thtrofli-20&marketplace=amazon&region=US&placement=1771470011&asins=1771470011&linkId=6ZPF7V22IC7NDGJA&show_border=true&link_opens_in_new_window=true

——–
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.

——–

Talk at #UCDavis: Standardizing Species: Listening to, representing, and universalizing bird sounds in the 20th Century

Talk: Standardizing Species: Listening to, representing, and universalizing bird sounds in the 20th Century

hui_10-21-14.pdf

Microbe-themed art of the month: Seung-Hwan Oh portraits w/ mold

OK this is pretty cool (from a microbe-art-science point of view): An Artist Who Paints Portraits With Mold | WIRED.  Seung-Hwan Oh “had to set up a micro-fungus farm in his studio” and he puts film in a warm wet environment (note to self – there could be a new human microbiome aspect of this project depending on what warm wet environment is chosen) and sometimes seeds the system with some mold.  And then he lets nature do its work.

See more about his Impermanence works here. (Really – check out the works – they are wild).

At that site the work is described in the following way:

The visual result of the symbiosis between film matter and organic matter is the conceptual origin of this body of work. The process involves the cultivation of emulsion consuming microbes on a visual environment created through portraits and a physical environment composed of developed film immersed in water. As the microbes consume light-sensitive chemical over the course of months or years, the silver halides destabilize, obfuscating the legibility of foreground, background, and scale. This creates an aesthetic of entangled creation and destruction that inevitably is ephemeral, and results in complete disintegration of the film so that it can only be delicately digitized before it is consumed.

Also see his Tumbl page where one can find many other images like this one:

Hat tip to Kate Scow for posting about this on Facebook.

——–
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.

——–

At #UCDavis: the UC #OpenAccess Policy & what it means for you (10/22, 1:30-3 pm)

The UC Open Access Policy and what it means for you (10/22 from 1:30-3pm)

A Discussion with Catherine Mitchell and Dr. Robert Powell on the UC OA policy
Date & Time: Wednesday, October 22, 2014 from 1:30-3:00pm
Location: Shields Library, Nelle Branch Room, 2nd floor (at the far end of the main reading room)

The UC Open Access Policy (http://osc.universityofcalifornia.edu/open-access-policy/ or http://uc-oa.info) was passed by the UC Academic Senate on July 24, 2013, and is going into effect for all UC campuses, including UC Davis, on November 1, 2014. The policy grants UC faculty the right to make their articles freely available to the public by depositing a pre-publication copy in an open access repository. What does this policy mean for faculty at UC Davis?

Come to this talk by Catherine Mitchell of the California Digital Library (CDL), who will describe the tools and services that CDL is developing to support the policy, and Dr. Robert Powell of Chemical Engineering, who will give background on the policy and its passage through the UC Senate. Afterwards a Q&A panel will be held with the speakers, UC Davis librarians and open access researchers to answer questions and discuss the implications of the policy and open access.

This talk is being held during Open Access Week 2014, an annual international event to raise awareness about open access issues.

Kids’ Microbiology Book Review: Germ Stories

I was going through some kids’ books today and found quite a few that I thought were wonderful and thought – well – I should post about some of them.  So that is what I am going to do.

The first I want to write about is Germ Stories by Arthur Kornberg with Illustrations by Adam Alaniz and Photos by Roberto Kolter.

 

I used to read it to my daughter all the time (she is two years older than my son) and then sometimes, when she was older, she would read it to my son.  A few things I like about this book:

  1. It is not all about pathogens – there are sections on yeast, penicillin, gut microbes and Myxococcus (although it is miswritten as Myxobacterium). 
  2. Everything is done as poetry / songs.  Some are cheesy, but my kids liked them.
  3. Each section on a different microbes has a little poem/song, a drawing, and a picture or two as well as a few mini facts (or I guess, micro facts). 
  4. The material is a bit scary / gross at times but not too over the top.
Anyway – I definitely recommend it if you want a microbiology book that will be good for reading to and reading by kids.

I added this book to a collection I am making via Amazon on “Microbiology Books for Kids“.  I will write about some of the other ones at another time.

//ws-na.amazon-adsystem.com/widgets/q?ServiceVersion=20070822&OneJS=1&Operation=GetAdHtml&MarketPlace=US&source=ac&ref=tf_til&ad_type=product_link&tracking_id=thtrofli-20&marketplace=amazon&region=US&placement=1891389513&asins=1891389513&linkId=Z6CIDKBFFZLZALSL&show_border=true&link_opens_in_new_window=true

UPDATE – Wanted other suggestions for good kids’ microbiology themed books …

——–
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.

——–

UC #OpenAccess policy comments wanted from Academic Senate members by 1/7/15

The University invites comments on the proposed draft Presidential Policy on Open Access, which is based on the Academic Senate Open Access Policy for all Academic Senate members adopted on July 24, 2013.

The proposed new policy extends open access rights and responsibilities to all non-Senate members of the UC community who are authors of scholarly articles, including faculty, other academic personnel, students, administrators, and staff. The policy allows non-Senate authors of scholarly articles to maintain legal control over their research articles while making their work freely available to the public. In addition, the proposed policy outlines procedures for implementing the policy for all UC authors, both Senate and non-Senate. Although the policy assumes all authors will make their scholarly articles available to the public, there is a procedure, which authors must undertake proactively, to opt out of the open access process.

The proposal is located on the UCOP Academic Personnel and Programs website, “Policies under review,” under the “Systemwide Review” tab at http://www.ucop.edu/academic-personnel-programs/academic-personnel-policy/policies-under-review/index.html. If you prefer these documents as attachments, please let me know.

Today at #UCDavis: Phillip Romero from UCSF: Data-Driven Exploration of Sequence and Function

Dr. Phillip Romero, UCSF
4:10 p.m. Chemistry in Rm 179
Seminar Title: “Data-Driven Protein Engineering: Learning the Sequence-Function Mapping from Experimental Data”