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 different species.


We are looking for candidates that are interested in doing both experimental and computational work and previous experience in  cell biology, microscopy, programming, image analysis and/or modelling of dynamical systems are all considered an asset. We will consider candidates that have a stronger expertise on either experimental or computational methods but are interested in learning and using both approaches. Additional information and application link is here with a closing date of 24 November 2013. We are available for further clarification in regards to suitability of background or information about the projects.

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 comments, at least for now, cannot be anonymous and in the pilot phase you have to be invited to join. It is also restricted to authors that have at least one abstract on Pubmed already. There are arguments in favour and against anonymity but I lean in favour of identifiable comments to keep the trolls at bay. In this way the comments are also associated to you (via your NCBI profile) and can be listed. Unfortunately NCBI accounts are still not possible to link to an ORCID ID but that should be easily fixed. You will be able to search articles that have comments are these will be made available through their APIs. 

I am sure there will be several criticism such as the fact that is invite only or that you are adding comments to articles that you might not even have access too. Overall, I think this is a great development.  Commenting systems have, for the most part, failed to work on the publishers side and the hope is that this might finally create a discussion forum with higher participation. The advantages here are a higher visibility and lower friction when compared with most publishers existing commenting systems. For ALMs it might be also very positive assuming this does increase the level of participation. I for one would like to have useful opinion attached to articles while I search for them online. 

You can get the whole back-story from this post by Rob Tibshirani and from many of other blog posts and press releases that I am sure will be hitting the web today. 

Project management (online) tools

I am currently looking for a tool to centralize project management across the group. I asked on twitter for suggestions and received a number useful tips. In case this is of use to others here are a few notes I took when exploring of few of these options. The features I am particularly interested are: low/no set-up or upkeep requirements, intuitive use, rich project notebooks with the possibility to add images and back-up support. Nice features to have: possibility to share with public; integration with Dropbox and/or Google Drive.

Here are the notes in no particular order with my preferences at the end.

Basecamp
Simple, intuitive and well designed project management and collaboration tool. Each project can have: project updates (activity list), text documents (simple text documents, cannot add images), To-do lists (linked to the calendar); discussion items (text and embedded images that can stand-alone or be linked to any other item including other discussions). Group view can quickly show you updates across all projects you are involved in. The group and projects view is great but it would be nicer to have notebooks within each project as implemented in Evernote. 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 activity. Marketplace with additional group and project widgets to add (eg. Group chat and wiki's). Free account 20MB limit with paid accounts starting at $2.5/month for 1GB up to $40/month for unlimited storage. Fairly cheap but  below average design and somewhat sluggish.

Evernote
This tool is centred on the idea of notebooks (collections of notes). Notes can contain text, embedded images, to-do lists, voice clips. Has a stand-alone program that facilitates copy-paste actions into the notebooks (mac and windows but works well under wine). Notebooks from free accounts cannot be edited by others. Premium accounts (£35 per year) can have notebooks edited by others. One premium account could be used to centralise group notebooks. Business accounts (£8.00/user/month) are needed to have group management features. Limited tools for group interactions (no comments, chat, activity dashboard) when compared with others.

Redmine
Free but but requires local installation. Fully fledged project management tool: activity, roadmap, issue tracker, gannt charts,calendar, news, documents, wiki, forum, files. Recommended by several people in twitter. I only had a quick look since I would prefer an online tool without set-up.

Trello
Card concept – Each card can have Activities (could be text description of project entries), to-do lists, files, can be assigned to specific people, due-dates,Attachments including google drive and dropbox. Cards can be stacked in groups, moved around, tagged with color codes, stickers and individuals responsible for them. It looks nice but I don't like the design for project management. Android and iOS apps. 10mb standard, 250mb gold (plus additional customization features) $5/month or $45 per year

Teambox
Dashboard concept; Users can be assigned to projects. Dashboard view has the list of tasks and notifications for the day. Projects can have activities, conversations tasks, notes, files and members. Notes would be were the project/sub-project/task notes could be added. Notes have version history and can be shared to public. Images can be embedded in the notes. Additional group tools: calendar , gantt chart, time tracking, video conference (by Zoom). Pro accounts also have workload and group chat. iOS and Android apps available. Free - 5 users/5 projects – Pro accounts are $5 per user per month (annual- 20% discount, two years – 30% discount) with unlimited projects. dropbox integration, workload views, group chat functionality and priority support.

Labguru
Project management with a specific focus on science labs. Very large number of features including: dashboard with activity feed, projects (organized into past/present/future milestones, notes with embedded and resizeable images, attachments, pubmed integration, automatic report generation), lab equipment/reagents inventory. Organizing science into milestones makes more sense than into tasks as it fits more the spirit of research versus engineering. Android and iOS apps meant to be used to follow protocols, take pictures, check storage, etc.  Overkill for a computational group.  Not very smooth as every action results in a full webpage refresh. Expensive ($12 per person/month, yearly billing).

Projecturf
Dashboard view and project view. Projects have: overview, calendar, tasks, tickets, time (could be useful for contract work or grant reporting issue), files, conversations and notes. Files can be integrated with Google drive and dropbox. Notes can have embedded images. Pricing starts at 5 projects, 5GB $20/month up to unlimited projects, 100GB for $200/month (1 month free for annual billing). Very directed towards engineering code based projects.

Summary
My favourites at this point are Basecamp, Teambox and Evernote. Evernote is clearly lacking as as group tool but has a nice focus on notebooks (as in lab notebooks). Basecamp is more polished and intuitive than Teambox but is missing a proper "notebook" within each project and is somewhat expensive. Teambox is not as well designed as Basecamp but should work well, is cheaper and has integration with Google drive. 

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.

So what does that mean ?  Is this a journal for large scale data analysis ? For the description of methods ? Not exactly. Reading the guide to authors we can see that an article "should not contain tests of new scientific hypotheses, extensive analyses aimed at providing new scientific insights, or descriptions of fundamentally new scientific methods". So instead one assumes that this journal is some sort of database where articles are descriptors of the data content and data quality. The added value of the journal would be to store the data and provide fancy ways to allow for re-analysis. That is also not the case since the data is meant to be "stored in one or more public, community recognized repositories". Importantly, these publications are not meant to replace and do not preclude future research articles that make use of these data. Here is an example of what these articles would look like. This example more likely represents what the journal hopes to receive as submissions so let's see how this shapes up in a year when people try to test the limits of this novel publication type.

In summary, articles published by this journal are mere descriptions of data with data quality metrics. This is the same information that any publication already should have except that Scientific Data articles are devoid of any insight or interpretation of the data. One argument in favor of this journal would be that this is a step into micro-publication and micro-attribution in science. Once the dataset is published anyone, not just the producers of the data, can make use of this information. A more cynical view would be that NPG wants to squeeze as much money as they can from scientists (and funding agencies) by promoting salami slicing publishing.

Why should we pay $1000 for a service that does not even handle data storage ? That money is much better spent supporting data infrastructures (disclaimer: I work at EMBL-EBI). There is no added value from this journal that is not or cannot be provided by data repository infrastructures. Yet, this journal is probably going to be a reasonable success since authors can essentially publish their research twice for an added $1000. In fact, anyone doing a large-scale data driven project can these days publish something like 4 different papers: the metadata, the main research article, the database article and the stand-alone analysis tool that does 2% better than others. I am not opposed to a more granular approach to scientific publication but we should make sure we don't waste money in this process. Right now I don't see any incentives to limit this waste nor any real progress in updating the way we filter and consume this more granular scientific content.