Science publishers' pyramid structure and lock-in strategies
It is not recent news that AAAS will start a digital open access multidisciplinary journal. It is called Science Advances and it will be the 4th journal of the AAAS family of journals. As I have described in the past this is part of trend in science publishing to cover wider range of perceived impact. Publishers are aiming to have journals that are highly selective and that drive brand awareness but also have journals that can publish almost any article that pass a fairly low bar of being scientifically sound. This trend was spurred by the success of PLOS One that showed that it is financially viable to have large open acc...
Source: Evolution of Cellular Networks - October 16, 2014 Category: Cytology Tags: publishing Source Type: blogs
Collaborative postdoc fellowship opportunities
I interrupt this long blogging hiatus to point out two potential postdoc fellowship opportunities to work with our group at the EMBL-EBI. One is the EIPOD program that is an EMBL wide interdisciplinary program. For this fellowship the project is collaboration with Nassos Typas (genetics) and Jeroen Krijgsveld's (proteomics) groups at the EMBL in Heidelberg. Successful candidates would be studying how Salmonella uses post-translational modification effector proteins to regulate and subvert the host cell. It is important to note that EIPOD applicants must be interested in doing both the computational and experimental as...
Source: Evolution of Cellular Networks - September 5, 2014 Category: Cytology Tags: positions Source Type: blogs
State of the lab, year 1 – setting up
I have used this blog in the past to keep track of my academic life where I can give a less formal perspective on papers I have published or ideas I am working on. Starting a group has made me think a bit about what I blog about. I have more responsibilities towards the people that have decided to work with me, towards the institution that has hired me (EMBL-EBI) and funding sources that support our work. At least for now I have decided to keep on sharing my personal view and in that context I though it could be interesting to write down my path as group leader in academia. This might become a yearly “thing”.I started ...
Source: Public Rambling - December 18, 2013 Category: Bioinformaticians Tags: academia Source Type: blogs
Introducing BMC MicroPub – fast, granular and revolutionary
I am happy to be able to share some exciting science publishing news with you. As you know, in the past few years, there has been a tremendous progress in open access publishing. The author-paying model has been shown to be viable in large part thanks to the pioneering efforts of BMC and PLOS. In particular PLOS One has been an incredible scientific and business success story that many others are trying to copy. Although these efforts are a great step forward they don't do enough to set all of the scientific knowledge free in a timely fashion. Sure you can publish almost anything today such as metadata, datasets, negative ...
Source: Public Rambling - November 1, 2013 Category: Bioinformaticians Tags: fiction publishing Source Type: blogs
Sysbio postdoc fellowship: spatio-temporal control of cell-cycle regulation
Funding is available for a 3 year postdoctoral fellowship to study spatio-temporal control in cell-cycle regulation. This is a join project between our group at the EMBL-EBI and the Quantitative Cell Biology group headed by Silvia Santos at the MRC Clinical Sciences Centre in London. More information about the groups interests can be found in the respective webpages.
The main objective of this project will be to study how the spatial and temporal control of key cell-cycle proteins change in different biological contexts. Examples of these different contexts include different differentiation states and/or differe...
Source: Public Rambling - October 29, 2013 Category: Bioinformaticians Tags: positions systems biology Source Type: blogs
Pubmed Commons - the new science water-cooler
Pubmed has decided to dip its toes into social activities by adding a commenting feature to it's website (named Pubmed Commons). It will start off in a closed pilot phase where you have to receive an invite in order to be able to comment but it should eventually be widely available. The implementation is simple and everything works as you would expect. Here is a screenshot with an example comment:
As you would expect you get an option to add a comment, to edit or delete previous comments you have made and up-vote other comments. In future versions you will be able to reply to comments in a threaded discussion. The comm...
Source: Public Rambling - October 22, 2013 Category: Bioinformaticians Source Type: blogs
Project management (online) tools
Discussions can be used as notebooks but they get mixed in with comments on any item such as a to-do list item. All projects can be downloaded for back-up but automation required 3rd party service or coding via the API. iOS app available and Android via 3rd party app. No free account (60 day trail), plans start at $20/month 10 projects 3GB limit up to £3000/year unlimited projects 500GB limit. Basecamp can be extended from a list of additional services (mostly 3rd party) and they tend to cost additional fees.
Freedcamp
Project views with to-do lists, discussions, milestones, file attachments. Dashboard view with group ac...
Source: Public Rambling - October 21, 2013 Category: Bioinformaticians Source Type: blogs
Scientific Data - ultimate salami slicing publishing
Last week a new NPG journal called Scientific Data started accepting submission. Although I discussed this new journal with colleagues a few times I realized that I never argued here why I think this a very strange idea for a journal. So what is Scientific Data ? In short it is a journal that publishes metadata for a dataset with data quality metrics. From the homepage:
Scientific Data is a new open-access, online-only publication for descriptions of scientifically valuable datasets. It introduces a new type of content called the Data Descriptor designed to make your data more discoverable, interpretable and reusable...
Source: Public Rambling - October 19, 2013 Category: Bioinformaticians Tags: publishing Source Type: blogs
Single-cell genomics: taking noise into account
Technical variation versus average read countsReprinted by permission from Macmillan Publishers Ltd Nat Methods, advance online (doi:10.1038/nmeth.2645)
Sequencing throughput and amplification strategies have improved to a point where single cell sequencing has become feasible. There was a recent review in Nat Rev Gen covering the progress in single cell genomics and some of its potential applications that is worth a read. However, the required amplification steps are likely to introduce significant variation for small amounts of starting material. A group of investigators from the EBML-Heidelberg, EMBL-E...
Source: Public Rambling - September 23, 2013 Category: Bioinformaticians Source Type: blogs
Interdisciplinary EMBL postdoc fellowship in genome evolution and chemical-biology
The EMBL Interdisciplinary Postdocs (EIPOD) program is now accepting applications (deadline 12 of September). This program funds interdisciplinary research projects between different units of the EMBL. Applicants are encouraged to discuss self-defined project ideas with EMBL scientists or select up to two project ideas available at the EIPOD website.
One of the project ideas listed this year is for a joint project between our group (EMBL-EBI) and the group of Nassos Typas at the EMBL Genome Biology Unit in Heidelberg. Here is a short description of project idea, entitled "Modeling genotype-to-phenotype relati...
Source: Public Rambling - July 2, 2013 Category: Bioinformaticians Source Type: blogs
Doing away with scientific journals
I got into a bit of an argument with Björn Brembs on twitter last week because of a statement I made in support of professional editors. I was mostly saying that professional editors were no worse than academic editors but our discussion went mostly into the general usefulness of scientific journals. Björn was arguing his positions that journal rankings in the form of the well known impact factor are absolutely useless. I was trying to argue that (unfortunately) we still need journals to act as filters. Having a discussion on Twitter is painful so I am giving my arguments some space in this blog post.
Björn ...
Source: Public Rambling - June 8, 2013 Category: Bioinformaticians Tags: publishing Source Type: blogs
EBI-Sanger postdoctoral fellowship on Plasmodium kinase regulatory networks
I am happy to announce a call for applications for a EBI-Sanger postdoctoral fellowship to study the kinase regulatory networks in Plasmodium. This is one of four currently open calls in the the EBI–Sanger Postdoctoral (ESPOD) Programme and the call closes on the 26th of July. This interdisciplinary programme is meant to foster collaborations between the EBI and the Wellcome Trust Sanger Institute, both at the Genome Campus near Cambridge UK. Our project is a collaboration between myself (EBI), Jyoti Choudhary (mass-spectrometry group leader at Sanger) and Oliver Billker (group leader a...
Source: Public Rambling - May 13, 2013 Category: Bioinformaticians Tags: positions Source Type: blogs
The case for article submission fees
For scientific journal articles the cost of publishing is almost exclusively covered by the articles that are accepted for publication. Either by the published authors or by the libraries. Advertisement and other items like the organization of conferences are probably not a very significant source of income. I don't want to argue here again the value of publishers and how we should be decoupling the costs of publishing (close to zero) from peer-review, accreditation and filtering. Instead I just want to explore the idea for a very obvious form a income that is not used - submission fees. Why don't journ...
Source: Public Rambling - April 7, 2013 Category: Bioinformaticians Tags: publishing Source Type: blogs
Benchmark the experimental data not just the integration
There was a paper out today in Molecular Systems Biology with a resource of kinase-substrate interactions obtained from in-vitro kinase assays using protein micro-arrays. It is clear that there is a significant difference between what a kinase regulates inside a cell and what it could phosphorylate in-vitro given appropriate conditions. In fact, reviewer number 1 in the attached comments (PDF), explains at length why these protein-array based kinase interactions may be problematic. The authors are aware of this and integrate the protein-array data with additional data sources to derive a higher confidence dataset of kinase...
Source: Public Rambling - April 2, 2013 Category: Bioinformaticians Tags: bioinformatics Source Type: blogs
The glacial pace of innovation in scientific publishing
Nature made available today a collection of articles about the future of publishing. One of these is a comment by Jason Priem on "Scholarship: Beyond the paper". It is beautifully written and inspirational. It is clear that Jason has a finger on the pulse of the scientific publishing world and is passionate about it. He sees a future of a "decoupled" journal, where modular distributed data streams can be built into stories openly and in real time. Where certification and filtering are not tied to the act of publishing and can happen on the fly by aggregating social peer review. While I wa...
Source: Public Rambling - March 28, 2013 Category: Bioinformaticians Tags: publishing Source Type: blogs
