Leading Research Organizations Announce Top-Tier, Open Access Journal for Biomedical and Life Sciences
The Howard Hughes Medical Institute, the Max Planck Society and the Wellcome Trust announced today that they are to support a new, top-tier, open access journal for biomedical and life sciences research.
The three organizations aim to establish a new journal that will attract and define the very best research publications from across these fields. All research published in the journal will make highly significant contributions that will extend the boundaries of scientific knowledge.
A team of highly regarded, experienced and actively practicing scientists will ensure fair, swift and transparent editorial decisions followed by rapid online publication. The first issue of the journal, whose name has yet to be decided, is expected to be published in the summer of 2012.
The three research organizations developed their plans following a workshop in 2010 at HHMI's Janelia Farm Research Campus attended by a number of leading scientists. The participants concluded that there was a need for a model of academic publishing that better suits the needs of the research community.
Dr. Robert Tjian, President of the Howard Hughes Medical Institute, says: "The message from the research community was clear: we are fortunate to have many excellent journals, but there is need for a different, more appropriate and efficient publishing model."
Professor Herbert Jäckle, Vice President of the Max Planck Society, says: "A journal which aims to represent and publish the very best research outcomes needs an editorial team of experienced – and, crucially, actively practicing – scientists. It must also be editorially independent of those who provide the financial support."
Sir Mark Walport, Director of the Wellcome Trust, says: "We will attract the most outstanding science for publication by establishing a journal in which researchers have confidence in robust editorial decisions taken by their scientific peers. This will be a journal for scientists edited by scientists. The ethos of the journal will be to avoid asking authors to make extensive modifications or perform endless additional experiments before a paper can be published."
Recruitment is under way for an Editor-in-Chief who – together with the journal's editorial team – will be an experienced, active scientist. The editorial team will be editorially independent of the funders. They will rely on their scientific expertise and active research experience to identify the best papers, make scientifically-based judgments and exercise leadership in steering these papers through peer review.
The journal will employ an open and transparent peer review process in which papers will be accepted or rejected as rapidly as possible, generally with only one round of revisions, and with limited need for modifications or additional experiments. For transparency, reviewers' comments will be published anonymously.
As the journal will only exist online, it offers an opportunity to create a journal and article format that will exploit the potential of new technologies to allow for improved data presentation. The journal will be an open access journal, i.e. the entire content will be freely available for all to read, to reproduce and for unrestricted use. This open access system will also enhance opportunities to share content and to more directly engage the reader.
The three organizations have made a commitment to cover costs of launching the journal to ensure its success. The long-term business model will be developed by the incoming Editor-in-Chief and the team they build.
Monday, June 27, 2011
New #openaccess journals welcome; competition good; not sure how they know it is "top tier" though
Sunday, June 26, 2011
Some pics of Ted the Titan Arum "Corpse Flower"
New #ucdavis store open on 2nd street
Thursday, June 23, 2011
Disclosures - we have disclosures - 23&me paper in PLoS Genetics
And opening up the paper revealed some interesting material before one even gets to the meat of the paper:
Funding: This study was funded by the participants, by 23andMe, and by a grant from Sergey Brin. Company CEO and co-author AW, wife of SB, has provided financial support to 23andMe for its general operational needs. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: CBD, JYT, ED, AKK, EMD, UF, JLM, AW, and NE are or have been employed by 23andMe and own stock options in the company. 23andMe CEO AW has provided general guidance, including guidance related to the company's research undertakings and direction. PLoS co-founder Michael B. Eisen is a member of the 23andMe Scientific Advisory Board.
Wednesday, June 22, 2011
I still love Dropbox - but maybe a little bit less right now
On June 19, 2011, we had a software bug that caused authentication issues. You can read more about it in our blog post. Our records show that your account wasn't improperly logged into during this time.
We are writing to you because one or more users you share a Dropbox folder with logged into their account during that period. We have no reason to believe that the login was improper, but in the unlikely event it was, there could have been access to the information in the following shared folder:
We are very sorry as this never should have happened. We are implementing additional safeguards to prevent this from happening again. If you have any questions please contact us at firstname.lastname@example.org
- (Name withheld by me)
- The Dropbox Team
Tuesday, June 21, 2011
Travel and meeting notes from #IndoorAir2011 in Austin Texas #microBEnet
About the meeting:
I got involved in helping organize a session at this conference as part of my microBEnet project. More on the planning and the meeting later but here are some quick notes just to get them out there. I wrote a bit about the run up to the meeting in the following posts:
- Indoor Air 2011 coming up in Austin, TX – still time to sign up ...
- Reminder – Indoor Air 2011 coming up June 5-10 Austin TX ...
- Indoor Air 2011; Austin, Tx; June 5-10 #microBEnet | Microbiology ...
- The Tree of Life: Off to #IndoorAir 2011 in Austin, TX - to ...
Below are some notes about the trip with twitter posts, pictures, and a few comments. I will post later with some more "scientific lessons learned" and such. But wanted to get this out there before I forgot details.
Headed out June 6.
Was going to head out June 7 but decided to head out late on June 6 so I could get to the meeting a bit earlier. I am posting my tweets below as a guide to the trip. Tweets are highlighted in yellow.
- Sacramento to Las Vegas to Austin to #IndoorAir2011#fb
Had a two plus hour layover in Las Vegas airport. What a horrible place with all the noise, the slot machines, and such. So I finally found a place that was reasonably quiet for dinner. Plus it had the hockey game on so I was happy.
Monday, June 20, 2011
A great moment for plant sciences: winners of HHMI-GBMF competition for Plant Science Program Investigators announced
Saturday, June 18, 2011
Some quick notes on #Synbio5: Synthetic Biology 5.0 at Stanford
1. Got invited by Natalie Kuldell in April to participate in an education workshop for the meeting. Eventually said yes, but only after deciding to not go to the Earth Microbiome Meeting in Beijing. I said yes in part b/c it was close by home but also b/c of the people Natalie invited to be on the panel. She wrote in the invitation email:
Other panelists who have confirmed their participation in this session are from Understanding Science/Understanding Evolution (Juday Scotchmoor), Nature Education (Ilona Miko), Science for Citizens (Darlene Cavalier), GenSpace (Ellen Jorgenson), and Hong Kong University of Science and Technology (King Chow).And well, of the ones I knew on the list, they all were great.
2. Had a conference call (very brief) in June to discuss the session.
3. Headed out to Stanford very late Tuesday night - and thus missed the Slam session that night. I got to my hotel at about 1:30 AM.
4. I woke up early enough to hop on my bike and ride on over to the meeting. I was a PhD student at Stanford and had brought my bike in the hopes of going for some rides around town. I took some pics on the way in:
Friday, June 17, 2011
Schwag from #synbio5 very popular at home #Amyris #igem
Twisted tree of life award: @Discovermag for article on Lynne Margulis
"A conversation with Lynn Margulis is an effective way to change the way you think about life. Not just your life. All life. Scientists today recognize five groups of life: bacteria, protoctists (amoebas, seaweed), fungi (yeast, mold, mushrooms), plants, and animals. Margulis, a self-described “evolutionist,” makes a convincing case that there are really just two groups, bacteria and everything else."
- Twisted Tree of Life Award #9: Nature News on the "Marsupial" platypus
- Twisted Tree of Life Award #7 #8: Alroy on "Changing the rules of evolution"
- Twisted Tree of Life Award: NPR on the Evolution of Crying
- Twisted tree of life award #6: Scientific American Origins piece for dissing microbes
- Twisted tree of life award #5: Nicholas Wade & use of higher, lower, ladders, etc
- Twisted Tree of Life Award #4: Hoxful Monsters Blog on "Primitive" Animals
- Twisted Tree of Life Award #3: The Columbus Dispatch on Ancient Bacteria
- Twisted Tree of Life Award #2: Science Friday on the Five Kingdoms
- Twisted Tree of Life Award #1: Salk Institute Press Release on Kinases
Thursday, June 16, 2011
More art & science - hand painted poster at Synthetic Biology #synbio5 - by Karmella Haynes
Karmella Haynes, had hand painted her poster on canvas. Drawn in by the art, I went to talk to her (well, first I said "This is awesome" or something like that. And then I found out a bit more detail. She had her paints with her and was continuing to add touches to the painting. Though I was fascinated by the art side of this, then we got to talking about the science because actually - the figures there were about work she had done on applying some ideas from synthetic biology to animal cells in tissue culture.
I was completely blown away by this. I am not sure if the same posters will be up tomorrow and if so I will try to get some better shots. Anyway, I found out she is on her way to a faculty position in Arizona and has recently been a post doctoral fellow at Davidson College.
Tuesday, June 14, 2011
Absolutely spectacular - glass microbes
Monday, June 13, 2011
Coming up on http://phyloseminar.org Jason Stajich (aka @hyphaltip) #fungi #genomics
Jason Stajich speaks Wednesday, June 29th at noon PST on "Fungal phylogenomics: Getting lost in the moldy forest."
Fungi occupy diverse ecological niches in roles from nutrient cycling in rainforest floors to aggressive plant and animal pathogens. Molecular phylogenetics has helped resolve many of branches on the Fungal tree of life and enabling studies of evolution across this diverse kingdom. The genome sequences from hundreds of fungi now permit the study of change in genes and gene content in this phylogenetic context and to connect molecular evolution with adaptation to ecological niches or changes in lifestyles. I will describe our work in studies contrasting pathogenic and non-pathogenic fungi and efforts to unravel the evolution of multicellularity in fungi comparing unicellular basal fungi with multicellular mushrooms and molds.
The development of tools for data mining and use of fungal genomics is also driving the pace of molecular biology and genetics of fungi. I will highlight new approaches to make this easier and the ways data integration can inform and transform studies of functional biology of fungi.
|Japan||04:00 (04:00 AM) on Thursday, June 30|
|New Zealand||07:00 (07:00 AM) on Thursday, June 30|
|West Coast USA||12:00 (12:00 PM) on Wednesday, June 29|
|East Coast USA||15:00 (03:00 PM) on Wednesday, June 29|
|England||20:00 (08:00 PM) on Wednesday, June 29|
|France||21:00 (09:00 PM) on Wednesday, June 29|
Learn how to connect ahead of time. To hear about upcoming talks, send an email to email@example.com or follow @ematsen.
If you can't make it, don't fret-- you can always watch the recording
Yes, I am a #RedSox & #PLoS fan; & this video sort of is proof #BenFranklinAward #OpenScience
And here are the slides I used. Will try to synch
For more on this award see
Sunday, June 12, 2011
How about this? Wash your hands. Please. (Nice video from SLV Health)
I note - my post originally said "Wash you hands" and my 6 year old daughter was snooping at my computer and said "Daddy, it says 'wash you hands' not 'wash your hands.'" Well, I think I found a new blog editor.
Opening up one’s eyes to other fields (cross-posting from #microBEnet)
I spend most of my time working on biology. I like to think I cover lots of breadth within biology and I probably do - microbes, evolution, ecology, human health, pathogens, symbioses, forensics, genomics, bioinformatics, and more. But nothing like really looking at other fields to realize how narrowly focused one is.
And that is what has happened to me since I took on the "microBEnet" project trying to foster communications and collaborations on microbiology of the built environment. I now pay much more attention to anything that might have a connection to "Building Science" in one way or another. Not only did I just go to an Indoor Air meeting, but I keep discovering more and more stuff right near home that I was not aware of before. For example - I just got sent this news link from Aaron Darling in my lab: UC Davis News & Information :: History of sciences in architecture subject of Mellon Foundation winner's study. Previously, I would definitely not have been paying much attention to architecture and history of science. But now seeing other people at UC Davis working on the Built Environment just makes me think about how I can build connections with them and talk to them about buildings (and other built environments) and possibly, one day, about the microbes that are in them.
Which brings me to another story. At the Indoor Air meeting earlier in the week in Austin, Texas, when heading to the conference center I got into a conversation with someone looking for the registration desk. After showing her where to go she asked where I was from and I said "UC Davis." And it turns out - she was too. Turns out, this was Deborah Bennett, who I had heard mentioned the evening before but had not heard the whole name. I just knew someone else at the meeting was from Davis. Deborah is at the UC Davis School of Public Health and works on some really interesting stuff. And since UC Davis is so big (some 2500 or so faculty I think) - it is not always easy or simple to find people even if you might have a connection to them.
So anyway, just a little commentary on how I find it fascinating to see for the first what was in a way right before my eyes.
Saturday, June 11, 2011
Fun with Ligercat: pubmed word clouds
So, of course, like many others, the first thing I did was search for myself:
Quick update (pics, twitter feed) on #IndoorAir2011 in Austin, TX #microBEnet
If you want some information about what happened at the meeting, best place right now is probably twitter
Also see the microBEnet blog which has some recent posts on this.
Thursday, June 09, 2011
Worst new omicsword, perhaps ever, the Dispensome #awful #badomics #reallybad #uggh
Wednesday, June 08, 2011
I like this pic of me so much it gets a whole post - "Apple Love" by Rhonda Roman
|Apple Love by Rhonda Roman|
Fortunately, she put her name on the back of the picture and a little googling and I found her photo collection on flickr. Her name is Rhonda Roman and I really like her collections there. But in particular I love this picture she took of me and Steven and others at the Market. It captures everything really about my interactions with Steve. Thanks Rhonda. A picture is worth way way more than 1000 words.
#UCDavis to partner with the Beijing Genome Institute (BGI)
For more on this breaking news see
- Chinese genomics giant BGI and UC Davis form partnership (Eurekalert)
- CHINESE GENOMICS GIANT BGI AND UC DAVIS FORM ... (BGI web site)
- Chinese Genomics Giant BGI and UC Davis Form Partnership
Monday, June 06, 2011
Off to #IndoorAir 2011 in Austin, TX - to discuss and promote http://microbe.net #microBEnet
Which brings me to Indoor Air 2011. We are also starting to organize or help organize some meetings and workshops to bring together the various folks who might be interested in microbiology of the built environment. And for Indoor Air we have helped the meeting organizer Rich Corsi plan some sessions on microbiology of the built environment. The sessions take place Wednesday and Thursday and should be great. Looking forward to going to Austin, maybe seeing some friends at UT and nearby (hint hint Dr. Hillis, Sheril K, etc) and learning about the built environment.
Sunday, June 05, 2011
Apparently, my own local paper hates my blog
Friday, June 03, 2011
Crosspost from http://microBE.net: New, massive volumes on #metagenomics coming out soon
- Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches.
- Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats
Order from Amazon:
Thursday, June 02, 2011
Sequence/short read archive (SRA) back from the dead
"Recently, NCBI announced that due to budget constraints, it would be discontinuing its Sequence Read Archive (SRA) and Trace Archive repositories for high-throughput sequence data. However, NIH has since committed interim funding for SRA in its current form until October 1, 2011. In addition, NCBI has been working with staff from other NIH Institutes and NIH grantees to develop an approach to continue archiving a widely used subset of next generation sequencing data after October 1, 2011.We now plan to continue handling sequencing data associated with:RNA-Seq, ChIP-Seq, and epigenomic data that are submitted to GEOGenomic and Transcriptomic assemblies that are submitted to GenBankGenomic assemblies to GenBank/WGS16S ribosomal RNA data associated with metagenomics that are submitted to GenBankIn addition, NCBI will continue to provide access to existing SRA and Trace Archive data for the foreseeable future. NCBI is also continuing to discuss with NIH Institutes approaches for handling other next-generation sequencing data associated with specific large-scale studies."
New #UCDavis Dean of the College of Biological Sciences: James E.K. Hildreth
- Harvard College, cum laude in Chemistry
- Rhodes Scholar
- PhD in Immunology from Oxford (I think)
- MD from Johns Hopkins
- Many major discoveries related to HIV. See for example:
Selfish DNA, symbionts and parasites - some quick links
- The Myth … of the Myth of Junk DNA (blog post by John Farrell)
- A formal theory of the selfish gene
- Capturing the superorganism: a formal theory of group adaptation.
- Bacterial toxin-antitoxin systems: more than selfish entities?
- Genomic islands: tools of bacterial horizontal gene transfer and evolution.
- A Brief History of the Status of Transposable Elements: From Junk DNA to Major Players in Evolution
- What traits are carried on mobile genetic elements, and why?
- Genomics and evolution of heritable bacterial symbionts.
- From parasite to mutualist: rapid evolution of Wolbachia in natural populations of Drosophila.
NSF requests for "conflicts of interest" lists drive me batty and seem to penalize collaborative, interdisciplinary researchers
I am working on a few proposals to the National Science Foundation where NSF asks one to include "lists of institutions, project personnel, and collaborators with Conflicts of Interest".
Seems simple I suppose. But not when you get down to the details. For example I found some guidance from the NSF about this where they ask one to list coauthors, collaborators, co-editors, students, advisors, advisees, friends, relatives, and many other affiliations.
To make a very long story short. NSF wants you to make a list of anyone who possibly should not review your grant. And if you are involved in many large collaborative projects or teach or train a lot of students. Well, you are screwed. For example, if they really want me to be thorough, I would probably have to list more than 500 people. This would include a few hundred co-authors and hundreds of collaborators (e.g., on some projects I am working on with the Joint Genome Institute there are hundreds of people involved in some way).
Wednesday, June 01, 2011
What's Lurking in Your (Work) Basement
They also had a nice food spread upstairs on the first floor of our building that I discovered later. The best part of this spread were the animal chocolates and carvings:
A good day for the Public Library of Science and science in general: #PLoS opens up search API
- Announcing the PLoS Search API – build innovative applications that accelerate science
- Fields in the PLoS Search engine
- some examples using the PLoS API
- PLoS API developers group
Crosspost from microBEnet: Where is metagenomic analysis heading? Hopefully in directions suggested in this paper.
|Figure 3 from Raes et al. Molecular Systems Biology 7 #473 doi:10.1038/msb.2011.6|
Am crossposting this from the microBEnet blog (microBEnet is the site for the microbiology of the built environment network that I am building):
Most recent post
Another day to think, to pause, to ponder.
Panorama of Sycamore Park and the memorial to Karim A bit over 10 years ago I wrote a blog post that I repost all the time. Entitled "...
I have a new friend in Google Scholar Updates I have written about the Updates system before and if you want more information please see...
New article out from the Eisen Lab: Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarumSee Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum Paper based on PhD thesis work of Katie Dahlha...
Just got this press release by email. I am sick of receiving dozens of unsolicited press releases, especially those in topics not related ...