Jonathan Eisen's Lab

I f$#@#ing love science but really f$#Ing hate travel much of the time

Well, have already written a bit about my fun trip to DC on Twitter and Facebook but thought I would sum it up here too. Last week I had to go to DC for a meeting relating to a Department of Homeland Security grant we have in my lab (it was the annual meeting of the program). Of course the point of the whole trip was to present about our work. And for the record – here are the slides for my talk I gave on Wednesday.

Bayesian Taxonomic Assignment for the Next-Generation Metagenomics from Jonathan Eisen

But alas, going to give talks is not just about the Science is it? It unfortunately is also about the travel. And boy do I hate travel most of the time these days. Here is a tale of my trip …. I was supposed to go on Monday but had to delay going until Tuesday due to illnesses in the family. So I called United and changed my flight and called the Westin in Alexandria and changed my hotel reservation and emailed the meeting organizers and let them know.

All seemed good. Then Tuesday AM I got an email from United saying my flight had been cancelled and I had been rebooked on another flight. After calling up United and finding out that the seat upgrade using my miles / Premier status was not available I at least confirmed that I would be getting in to DC not too late. And so after lingering at home I headed to the airport and got on the flight from SMF to Houston.

I got to Houston, walked around for a while and eventually made my way to the connection to DC. I went to board and the machine gave the ticket agent an error message saying “Passenger is not ticketed for this flight” or something like that. Great. And I had to leave the line, go to the desk and wait a bit until someone helped me. There I found out that United had somehow cancelled the entire rest of my flight and thus I was not only no longer booked on a flight to DC I had no return flight either. After a painful but brief delay somehow they put me on the connection and I got to DC.

It was after getting the error message that I ended up engaging some social media to express my frustration and I tweeted about United. And eventually the United Twitter handler got back to me and helped me confirm that I did now have a return flight.

Anyway – I moved on past the United issue and got in a cab in DC and headed to the Westin Alexandria. I got there and checked in. Sadly I found out there was no food available anywhere at the hotel (it was only 10:50 PM or so). So I decided to just go up to my room and crash. I went up to my room and – well – was seriously in for a shock. My room was a meeting room of some sort overrun with meeting tables and with a small, rollaway bed smushed up against the wall.

Oh my God. You have got to be kidding me. I have serious trouble sleeping when I travel and am not exactly the smallest guy in the world. A rollaway bed in the middle of a conference room? Uggh. So I called up the front desk and asked

“Is this some sort of mistake. Is there supposed to be a bedroom connected to this room?“

And the person from the desk said “No. That is your room.”

And I said “Well, I can’t sleep on that bed“

And he said “Sorry – we are fully booked – that is all we have.”

And I said, again “Listen, I called yesterday and confirmed my room and told you I was coming late and this is not acceptable. I want a normal bedroom with a normal bed. Nothing fancy. Just a bedroom.“

And he said “OK. I have another room.”

So I said “Can someone bring up the key?“

And he said “No. There is no one else here.“

So I said “OK I will come back down.”

So I got my stuff and went back down and really wanted to ask “Well, why is there a room now if you told me the room with the rollaway bed was the last room” but I held my tongue. And after a computer malfunction that led to a 5-10 minute wait he gave me a new room key.

And I was off again. Once there, I opened the door to the room and I knew before even getting into it why they did not give it to me at first. It reeked of cigarette smoke. Like someone had a cigarette testing party in the room. Drowning in smoke smell. I took a pic of the air vents to represent the smell … for what that was worth. So I immediately went to the phone and called the desk again.

Me: “Hey it’s the guy who you just gave a new room to. This room is even worse. Unbearable cigarette smell here. Is this a smoking room?”

“No we don’t have smoking rooms.”

Me: “So did the cleaning crew mark this room as having been smoked in and you gave it to me even though it has not been cleaned yet without telling me?“

Answer “No.”

Me “I need a different room.”

Him: “Ok – let me look. (click click click). OK I have another room“

Me: “Can someone bring the key up?“

Answer: “I don’t think so.”

Me: “OK I will come back down.”

So down I went and finally got a third room.

And this one was OK. Meanwhile I was also positing details of the debacle to Twitter and Facebook. And enjoying (in a theater of the absurd kind of way) some of the responses I got from miscellaneous people and also the communications with the Westin Twitter handler. Here below is a Storify of some of the communications around both the United issue and the Westin issue.

//storify.com/phylogenomics/i-f-ing-love-science-but-f-ing-hate-travel-much-of.js[View the story “I f#ing love science but f#ing hate travel much of the time” on Storify]

But perhaps the most entertaining part were the DM messages from the @Westin person. Here is the thread – copied and pasted from Twitter

@Westin: 1/2 We do apologize for the inconvenience. We spoke to the hotel and was informed that you have been shifted to another room
@Westin: 2/2 with a king bed. Please let us or the front desk know if you need any further assistance.
Me: Third try … Why wouldn’t the cleaning crew inform them of the smoky room? It was awful
Me: And why would they give me a room with a rollaway as the only bed without saying anything?
Me: I would like to formally request a free night in exchange for this absurdity
@Westin: 1/3 We truly apologize for the inconveniences.Your booking was made through a group rate & that was originally the room type booked for you.
@Westin: 2/3 Unfortunately, we are unable to grant you that request as hotel has accommodated by shifting rooms for you to a king bed. We spoke to
@Westin: 3/3 the hotel regarding the strong smell next door as there are no smoking rooms at the hotel. Someone will reach out to you in the morning.
Me: ????- are you saying they booked me a room with a rollaway bed?
Me: Are you saying the room did not smell of smoke ???
@Westin: We understand your frustration & do apologize again for the inconvenience. The management team will reach out to you in the morning to
@Westin: further follow up on your concerns as they are in the best position to address situations. Please feel free to let us know if you require
@Westin: any additional assistance from our team

I spent a few hours working on my talk and then finally got a little bit of sleep. In the morning I ordered room service. An espresso, and eggs and toast. I asked for fried eggs and got scrambled. I did not want meat but got some. I asked for water and got none. But I never mentioned this to the hotel. Seemed kind of pointless.

And then I had an email exchange with a representative of the Westin Alexandria that ended up being somewhat interesting.

Westin

Good Morning Mr. Eisen,

I have received your feedback from our corporate office in regards to your check-in experience last night.

First of all, please allow me to apologize on behalf of my team and the hotel for the inconvenience you went through last night. Our hotel was closed to sold out last night so there were some challenges in the room assignment with the preference of each of our guest.

I also meant to touch base with your directly this morning but I have noticed you have already departed the hotel.

I will go ahead and take care of your night for the inconvenience you went through and it will also be my pleasure to recognize you as a loyal SPG member by giving you a credit of 5,000 SPG Points.

If there is anything further I can assist you with, please feel free to contact me directly. I hope you will choose us again for your future travel plan in Alexandria. When you do so, please let me know so I can review your accommodation.

Once again, my sincere apologies for the inconvenience.

Be Well,
Thomas

THOMAS
POTEAU
Director of Operations
THE WESTIN ALEXANDRIA
400 Courthouse Square, Alexandria, Virginia 22314

Thanks for the email.

I appreciate what you have done. I would very much like to know of you can give me some explanation of what happened – like why was I sent to a room with a rollaway bed with no warning or explanation. And whether the second room I was sent to was empty because of the smoke smell and if so why I was sent there?

Thanks

Jonathan Eisen

Westin:

Mr Eisen,

In a sold out situation like last night, we review the last arrivals and room assignment and with your SPG status, my front desk supervisor upgraded you to our hospitality suite. Yes this is a room which doesn’t have a permanent bed so we put a rollaway in this room, however this is a much larger room (suite) than our Traditional King. Most of our guests usually don’t mind the situation and actually enjoy the larger room. Since our rollaway beds are heavenly beds like any of our beds, the size of the bed is the only difference and most of the time acceptable with our guests.

That being said, yes, we should have been proactive and contact you to verify the accommodation, informed you during the registration of the situation and being accommodating in taking care of your rate knowing it was an inconvenience for you. My apologies for that, I have addressed it with my team this morning.

As far as the smoking room, again when we only have a couple of rooms available, it becomes much more challenging. The room had been treated for smoke for the last 2 days by the housekeeping team and was turn back to market due to our occupancy level. When our system assigned you that room, the agent didn’t know that room had smoking issue since it was back in his system as an available room.

I personally walked this room this morning and confirm the smell was still very much a discomfort. I have removed the room from our inventory for further treatment.

Once again, I am sorry for the inconvenience and hope you will come back to stay with us again in the near future so I can personally make sure we provide you with the service levels Westin offers.

Be Well
Thomas

THOMAS
POTEAU
Director of Operations
THE WESTIN ALEXANDRIA

Thanks very much for the further explanation. I note – IF someone had said that that was a heavenly bed I might have tried it, but I have extensive experience with rollaway beds because I have two kids. And the rollaways are almost always unusably by me. So perhaps when you inform the people what to do they should say “We only have a rollaway bed BUT it is comfortable and is a Heavenly bed. That might have made everything fine … but without that knowledge I just thought I got screwed …

Jonathan

Westin

Thank you. I agree and I will certainly take on the feedback and share with my team so we can better explain it to our guest.

THOMAS
POTEAU
Director of Operations
THE WESTIN ALEXANDRIA

So then – finally it seemed resolved. Not only would my room be free but perhaps they learned something and would do a better job next time. And finally I got to give my talk.

//storify.com/phylogenomics/dhs-talk.js[View the story “DHS talk” on Storify]
I note – the return trip was OK. United let me change my flight to an earlier one. I got home in time to read to my kids before they went to sleep. And other than being exhausted and still a little peeved, I think it went OK.

Article by Amy Maxmen "Preserving Research" on ways to share unpublished manuscripts

There is a nice article by Amy Maxmen in The Scientist titled “Preserving Research” on ways to share unpublished manuscripts. It includes some discussion of pros and cons of various archives including arXiv, Figshare, ResearchGate and more. Definitely worth a look. There are of course many many many ways to share your articles before and after you publish them.

For more about sharing PDFs/articles see my post: The Tree of Life: Ten simple ways to share PDFs of your papers. And of course, don’t forget that just posting your paper somewhere does not mean that it will continue to be available to all. Also – the license that you use when sharing your article affects how people can use and reshare it so pay attention to the fine print and use as broad a license as possible …

RFA Announcement – International Cooperative Biodiversity Groups (ICBG)

Forwarding this from ASM



RFA Announcement – International Cooperative Biodiversity Groups Dear Colleague: The Department of Health and Human Services, National Institutes of Health (NIH) and National Science Foundation (NSF) have requested that ASM bring to the attention of interested members the following RFA: Limited Competition: International Cooperative Biodiversity Groups (U19) Application Due Date(s): November 20, 2013, by 5:00 PM local time of applicant organization. URL: http://grants.nih.gov/grants/guide/rfa-files/RFA-TW-13-001.html Synopsis: The National Institutes of Health and the National Science Foundation invite applications for the establishment or continuation of “International Cooperative Biodiversity Groups” (ICBG). The program is built on the observation that natural products derived from organisms in nature remain the most productive source of new therapeutics, yet the biodiversity on which discovery of these drugs depends is rapidly disappearing around the world. Consequently, the ICBG program supports international, public-private, interdisciplinary research teams in the exploration and discovery of novel compounds and extracts with potential for development as therapeutic agents for multiple disease targets, at the same time as it builds research capacity in partnering countries to support sustainable exploration and use of biodiversity and the knowledge to conserve it. These goals are advanced through fair and equitable partnership frameworks among research organizations in the U.S. and in low and middle income countries (LMICs). This competition of the International Cooperative Biodiversity Groups (ICBG) program continues several new emphases that began with the previous FOA, RFA-TW-08-010, including an emphasis on microbial and marine organisms, greater involvement of funded consortia with government contract resources, and greater use of molecular and genomic tools. This FOA also introduces some new features, including some new target health areas (neurological disorders and stroke, pain and inflammatory processes, and others, see Interests of NIH institutes and Centers, below) and an emphasis on supporting the scientific basis for integrated conservation and development efforts through research and research training rather than through direct implementation activities. Award Information: Funds Available and Anticipated Number of Awards: Issuing agencies and partner components intend to commit an estimated total of $3.3 mil for Fiscal Year 2014, corresponding to an estimate of 3-4 awards. The number of awards is contingent upon NIH appropriations and funds availability as well as the submission of a sufficient number of meritorious applications. Future year amounts will depend on annual appropriations. Award Budget An applicant may request a budget for direct costs up to $700,000 per year. Award Project Period An applicant may request a project period of up to five years. Sincerely, Ronald M. Atlas, Ph.D. Chair, Public and Scientific Affairs Board

	American Society For Microbiology © 2013

Computational Biologist job posting at 10X technologies

Interesting job posting I just got sent by 10X technologies:

Computational Biologist

10X is looking for an outstanding individual to join its Computational Biology group. This person will: (1) lead the development of algorithms that form the core of 10X software and (2) define custom analyses to guide product development. This position is a unique opportunity to work on an exciting and novel form of Next Generation Sequencing (NGS) data that enables a wide array of previously unachievable applications. The ideal candidate will have an extremely strong background in algorithms and statistics and will be highly proficient in both generating novel algorithms and combining them with existing tools.

The right candidate must also have strong programming skills, and a keen interest in biology and working with real-world data. Strong interpersonal skills, a desire to understand customer needs and the ability to communicate results clearly are a must. This position will interact closely with colleagues in biochemistry, microfluidics and chemistry.

Key Responsibilities

Develop algorithms for novel NGS data across a number of novel applications
Develop custom analyses to asses and guide development of the core technology
Work with software team to commercialize algorithms products
Work with early customers to understand applications and requirements
Analyze internally generated sequencing data
Desired Skills and Background

PhD in computer science, mathematics, computational/systems biology or related field
Extremely strong background in algorithms and statistics
Strong programming ability in Python (experience with C/C++ a significant plus)
Hands on experience with NGS data tools (e.g. bwa, samtools, GATK)
Creative problem solver who obsesses over novel applications of data
A deep intuition for the processes utilized by current NGS technologies
A combination of mathematical depth with a healthy respect for the imperfections
inherent in real-world data
Highly independent
Ability to work in a fast-paced and quickly changing environment
For more information, please contact jobs

10XCompBioJobDescription.pdf

Great use of metagenomic data: community wide adaptation signatures

OK I have been dreaming about doing something like this for many years. One of the potentially most useful aspects of shotgun metagenomic data is that you get a sample of many/all members of a microbial community at once. And then in theory one could look across different species and taxa and ask – do they all have similar adaptations in response to some sort of environmental pressure. There have been a few papers on this over the last few years (e.g. check out this one from Muegge et al on Diet Driving Convergence in Gut Microbes). But this new paper is really the type of thing I have been hoping to see: Environmental shaping of codon usage and functional adaptation across microbial communities. Basically they looked at codon usage in organisms in different metagenomic samples and found major metagenome specific signatures, suggesting that different taxa were in essence converging on common codon usage.

The paper is definitely worth a look.

Ewan Birney visiting Davis, speaking at the Genome Center next Wednesday (14th August)

Forwarding this announcement i just received

Ewan Birney, the Associate Directory of the European Bioinformatics Institute, is visiting UC Davis next Wednesday and will be giving a talk at 2:00 in the GBSF Auditorium: ‘Using outbred genetics to understand basic biological processes’.
He will also talk about the need for a data infrastructure in the life sciences and how the European Bioinformatics Institute contributes to it.

Ewan is the creator/co-creator of many popular bioinformatics tools (e.g. GeneWise, CRAM, Velvet, Pecan), and has had an enthusiastic involvement in many other genomics/bioinformatics projects (e.g. Pfam, BioPerl, Ensembl), not to mention taking a leading role in the human ENCODE project.

Lab tech (level 3ish) in population genetics looking for job in Davis

I have a friend of a friend who has almost 20 years of experience as a technician working in population genetics and forensics. She has just moved to Davis and is looking for work, she came highly recommended from her previous lab. If anyone knows of any position she might look at, or anyone to contact please let me know. I can also send a resume on request.

News coverage of SpaceMicrobes event

Quick post here. Our Project MERCCURI got some press coverage relating to an event July 20th with the Arizona Cardinals: Gilbert, Tempe participate in national microbe-swabbing project – East Valley Tribune: Gilbert.

From the article:

“The event — held at the Arizona Cardinals’ training facility on July 20 — featured members of the Cardinals’ cheerleading squad swabbing their shoes and cell phones to collect microbe samples later sent to a lab at the University of California Davis for analysis. Microbes are microscopic single-cell organisms that have existed for millions of years and are found just about everywhere on the planet.”

Also some mention of out sampling the Space Station and other parts of the project.

See more about the project here.

Perhaps this meeting should be renamed "Of Microbiomes and Men" ….

Well, just got an email inviting me to participate in a meeting on microbiomes. The full invite is at the bottom of this posting. Alas, at first glances it seems this meeting, has, well, some gender issues.

Confirmed Keynote Speakers: both male.

Mark Adams, Ph.D., Scientific Director, J. Craig Venter Institute, San Diego
Sarkis K. Mazmanian, Professor of Biology, California Institute of Technology

Confirmed other speakers: all seven male

Pierre Belichard, Co-founder and CEO, Enterome
Adam Godzik, Ph.D., Bioinformatics and Systems Biology, Professor & Program Director, Sanford-Burnham Research Institute
JunHua Li, Team Leader of Reference Metagenomics, BGI Research
Victor Nizet, MD, Professor & Division Chief, Department of Pediatrics, UCSD School of Medicine, San Diego
Steve Orndorff, NuMe Health
Andrei Osterman, Ph.D., Professor, Bioinformatics & Systems Biology, Infectious and Inflammatory Disease Center, Sanford-Burnham Medical Research Institute
Bernd Schnabl, MD, Assistant Professor, Division of Gastroenterology, UCSD School of Medicine, TSRI California Campus

I suppose one could say “Well, they are still working on their agenda … maybe they will have some female speakers.” So I decided to dig around a little bit more. They provide a link to the outline agenda here. Alas that is even worse. There we find out who some invited speakers are who have not yet accepted

David Odelson, R&D Program Director, Life Technologies
Peter B. DiLaura, President & CEO, Second Genome
Chris Christofferson, Morganthaler Ventures
Lou Tartaglia, Third Rock Ventures
Mike Grey, Pappas Ventures
Justin L. Sonnenburg, Assistant Professor, Microbiology & Immunology, Stanford School of Medicine, Palo Alto, CA

So that is 9 confirmed speakers and six invited speakers – all of whom are male. Great. Here is a suggestion. DO NOT GO TO THIS MEETING.

The Microbiome / Microbiota R&D and Business Collaboration Forum
Special August Registration Discount SAVE 15%

use discount code NN/AUG15/AL
Keynote speakers:
Mark Adams, Ph.D., Scientific Director, J. Craig Venter Institute, San Diego
Sarkis K. Mazmanian, Professor of Biology, California Institute of Technology

Dear Jonathan

The announcement in June that Johnson & Johnson is collaborating with Second Genome, one of the first biotech companies focused entirely on the human microbiome, is, according to Forbes magazine, a turning point at which “big Pharma” money begins to back this new field of research.

The 1-2 kilograms of bacteria living inside, and on the surface of, all human beings – the Human Microbiome – constitutes both another “human” organ and a third protective “immune system” after the innate and adaptive immune systems. This mix of good and bad bacteria, long a subject of academic interest, has been linked to everything from infectious diseases like clostridium difficile to obesity and even mental health. Now that the commercial potential of this field of research is being recognized it is attracting venture capital and other funding.

The developments in research and the commercial possibilities are the subject of The Microbiome/Microbiota R&D and Business Collaboration Forum, which will take place in San Diego onOctober 7th & 8th 2013.

Any questions? email nnoakes@globalengage.co.uk or telephone +44 (0)1865 849841

Confirmed Keynote Speakers

Mark Adams, Ph.D., Scientific Director, J. Craig Venter Institute, San Diego

Sarkis Mazmanian
Sarkis K. Mazmanian, Professor of Biology, California Institute of Technology

Confirmed Speakers

Pierre Belichard, Co-founder and CEO, Enterome
Adam Godzik, Ph.D., Bioinformatics and Systems Biology, Professor & Program Director, Sanford-Burnham Research Institute
JunHua Li, Team Leader of Reference Metagenomics, BGI Research
Victor Nizet, MD, Professor & Division Chief, Department of Pediatrics, UCSD School of Medicine, San Diego
Steve Orndorff, NuMe Health
Andrei Osterman, Ph.D., Professor, Bioinformatics & Systems Biology, Infectious and Inflammatory Disease Center, Sanford-Burnham Medical Research Institute
Bernd Schnabl, MD, Assistant Professor, Division of Gastroenterology, UCSD School of Medicine, TSRI California Campus

This first-in-class, microbiome-focused hybrid R&D and business conference attracting 150 attendees from all over the world, plus an exceptional speaker faculty, will provide an interactive networking forum to both further research and commercialization opportunities. It also aims to answer your queries through a vibrant exhibition room full of technology providers showcasing their R&D platforms & services; as well as via scientific poster sessions; expert-led case-study presentations; and interactive Q&A panel discussions.

The Outline Agenda

www.globalengage.co.uk/microbiome/MicrobiomeAgenda2013.pdf

Sequencing/Bioinformatics of the Microbiome

An overview of the human microbiome project
Contributions to Metagenomics and Data Analysis
Advances in sequencing technologies
The role of chip technologies (the Phylo chip) as a rapid readout vs. sequencing
The $1000 genome may cost $100Ms to interpret!

Venture Capital + Technology Transfer

Commercializing Microbiome Technologies from Government & Academic Entities
International Small Company Showcase

The microbiome of the GI tract

The role of commensal bacteria in regulating the immune system
Metabolic exchange in gut microbial communities: who needs vitamins?
Contemplating novel antibiotic therapies that do not destroy the healthy microbiome
Metagenomic profiling in IBD

Clinical Applications

The contribution of the gut microbiome to liver disease
Treatment of C. Difficile infections with fecal transplants

Connections to the Food World

The role of diet in regulating the microbiome mix
Prebiotics vs. probiotics vs. pharmaceuticals
Opportunities to treat diabetes and obesity via the microbiome
Panel Discussion – Pharma/Biotech/Food Industry Partnering
Small Company Showcases

www.globalengage.co.uk/microbiome.html

Not interested in the Microbiome/Microbiota?
Unsubscribe here

Nick Noakes: nnoakes@globalengage.co.uk Tel +44 (0) 1865 849841
Global Engage, The Kidlington Centre, Kidlington, Oxfordshire, OX5 2DL, UK.

You might think that at some point some of the people organizing meetings

Graduate Student Opportunity in Marine Biology /Environmental Sequencing of micro eukaryotes

Posting a grad student opportunity for a new project I’m involved in – The project will be using high-throughput sequencing techniques to study microbial eukaryotes in Arctic sediments.

Graduate Student Opportunity in Marine Biology / Biological Oceanography
UAF School of Fisheries and Ocean Sciences, Fairbanks, Alaska USA

We are seeking a graduate student research assistant for a project applying high-throughput DNA sequencing techniques in the study of meiofaunal communities in the Arctic. The student will take a lead role in sample processing and data analysis, including both standard microscopic analysis and morphological taxonomy and high-throughput sequencing approaches. Data will be used to assess meiofaunal community structure and diversity in the US Arctic, and identify possible environmental drivers of community structure. Skills developed will include DNA extraction, purification, and next-generation sequencing methods, and analysis of sequence data. Prior experience in molecular methods is desirable, but not essential. The student may also have the opportunity to participate in research cruises in the Arctic.

Prospective students are encouraged to apply at either the MS or PhD level (PhD candidates would be expected to develop additional research objectives that complement the project, and to work with the advisor in pursuing additional funding sources). The position will be based at the University of Alaska, Fairbanks, but the student will be expected to travel for extended periods to University of California, Davis to receive training in sequencing methods and data analysis. Funding is available for 2.5 years, including tuition, stipend (starting at ~$21,000 / year for MS students), and basic health insurance. The successful candidate will be expected to enroll in the graduate program in Spring 2014, but may be hired as a staff research technician as early as Oct. 1, 2013 if available.

To apply:
Application materials and general information about the graduate program are available at http://www.sfos.uaf.edu/prospective/graduate/. Application deadline for spring enrollment is October 15, 2013. Required materials include three letters of recommendation, general GRE scores, and transcripts from all institutions attended. If interested, or for additional information about the project or the position, contact Sarah Hardy (smhardy@alaska.edu) or Holly Bik (hbik@ucdavis.edu).

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