Much has happened since the last blog entry. Happy new year ;-)

We've recently released the Twitter streaming library that we've been using for over a year now. It's available at https://github.com/salathegroup/mkondo. In a nutshell, this is the code that we are currently using to connect to Twitter to collect data, back off if we ask for too much data, and store and back up the data, with a few other useful features. Shashank Khandelwal who has been writing the code will write a few words about the library in another post. For now, the readme file is quite self-explanatory. 

In other news, I (MS) have embarked on a new path toward radical open access publishing. In a nutshell, I'm working on a new project and decided to make everything open access from day one. By everything I mean, well, everything: Both code and paper in progress are hosted over at GitHub, which has the added benefit of everyone being able to follow every change I make to either the code or the paper as I'm writing it. On top of that, there's a special blog that chronicles the entire experience. I'm pretty excited about the format (if you're interested why, check out the first post on the project blog).

As 2011 is slowly winding down, it's time for some thoughts on what has been and what hopefully will be. It's been a fantastically crazy 2011 and I feel very privileged to be working on something that is both interesting, exciting and relevant at the same time. 

It's good enough to work on one interesting problem, but I've been fortunate enough to be able to work on two this year. On the one hand, the work on using sensors to measure contact networks has been very interesting, and to be able to continue and expand this line of work with support from the CDC is scientifically and personally very satisfying. On the other hand, the work on using social media for epidemiology has been so much fun I can't even begin to describe it. Building on these two lines of work, we have very ambitious plans for 2012, and I can only hope that all of us in the group manage to keep their sanity :-) 

Personally, the Data Science & Epidemiology workshop has been one of the highlights this year. I'm very much hoping that we can do something similar in the not too distant future, either at the CIDD or at some other place. I'm a big fan of modern communication technology (needless to say), but there is something about putting a few like-minded people in a room to think about a problem they deeply care about that just cannot be replaced with even the best communication technology. 

The challenge for 2012 will be saying no - to focus on the most important things only. There are so many potential projects, so many tempting funding announcements, so many interesting conferences that we'd need 48 hour days to even catch up. Hopefully we'll make the right decisions. Being able to talk at the Strata Conference next year and at the Santa Fe Institute Science Board Symposium will certainly be highlights that I'm already very much looking forward to. 

UPDATE Nov 16: code is at https://github.com/salathegroup/vaccine-sentiment

Our paper on Twitter vaccincation sentiments is out. We were made aware of that fact just a few hours ago and haven't had the time to get the data ready for public access on this website. We're very committed to open data and want to share all the data that we have, including the code used in the study (code for data collection, machine learning, and simulations). Further, we have to make sure that we anonymize the data sufficiently to be in line with Twitter's terms and coniditions. Stay tuned, the data will be online here on this website (under publications) very soon.

I'm very happy to join the PLoS Computational Biology editorial board as an Associate Editor. I've been acting as a guest editor for a few times now, but making the jump to officially join the board is very, very exciting.

There is no doubt that PLoS has fundamentally changed the publishing landscape, and clearly for the better. Scientific research should be open at all levels. I'm a strong proponent of open access to code and data (whenever legally possible), and an even stronger proponent of open access to the research articles. My own personal commitment to this cause is manyfold. First, I always try to make the article open access - either by publishing in an open access journal, or by paying the extra fee to make the article open access whenever this is possible. Second, all our data will be made accessible by default upon publication of a research article (we've been doing this for a while now). Finally, we have recently started using Github to make all programming code used for analysis and simulations publicly available.

But open access is not the only thing that excites me about PLoS Computational Biology - it's the breath and quality of research that they publish. Here are just a few fascinating examples that are close to my personal interests:

Infectious Disease Modeling of Social Contagion in Networks
(Alison L. Hill, David G. Rand, Martin A. Nowak, Nicholas A. Christakis)

Simulated Epidemics in an Empirical Spatiotemporal Network of 50,185 Sexual Contacts
(Luis E. C. Rocha, Fredrik Liljeros, Petter Holme)

Evolutionary Establishment of Moral and Double Moral Standards through Spatial Interactions
(Dirk Helbing, Attila Szolnoki, Matjaž Perc, György Szabó)

A Dynamic Network Approach for the Study of Human Phenotypes
(César A. Hidalgo, Nicholas Blumm, Albert-László Barabási, Nicholas A. Christakis)

Social Contact Networks and Disease Eradicability under Voluntary Vaccination
(Ana Perisic, Chris T. Bauch)

My own experience in publishing with PLoS Computational Biology has been mostly very positive. I'm particularly excited about our upcoming paper, "Assessing Vaccination Sentiments with Online Social Media: Implications for Infectious Disease Dynamics and Control" (currently available as prepublication PDF, but very soon online at the PLoS Computational Biology website).

All in all, a great opportunity I'm very much looking forward to. 

I'm really excited about the upcoming movie Contagion (watch trailer below). The trailer captures much of the excitment that I feel about my own research topic. I can't remember seeing a trailer of a Hollywood movie that had references to so many of the issues we are dealing with in our group: disease, biological contagion (virus), social contagion (fear), contact networks, public health, spatial spread of disease, vaccines, evolution, mutation, virulence, you name it.

On top of that, some of my favorite actors: Gwyneth Paltrow, Lawrence Fishburn, Matt Damon. Direct by Steven Soderbergh? Can't get any better than that.

Position filled, thanks to all interested! 

A postdoctoral position is available within our group at the Center for Infectious Disease Dynamics (CIDD) at Penn State University.

We are conducting a two-year study on social networks and disease dynamics in school settings with the aim of understanding infectious disease spread at an unprecedented level. We are a multi-disciplinary team experienced in surveying methods, wireless sensor network technology, mobile phone application development, molecular genetics, and mathematical and computational modeling of disease dynamics. We are looking for a postdoctoral researcher who will execute this highly complex project at the interface of the biological, computational and social sciences, and which will involve thousands of human subjects.

The successful candidate is enthusiastic, creative, and highly organized, with a track record of successfully completing projects that require strong organizational and project management skills. An engaging, motivating and trustworthy personality, and “people skills” in particular, are necessary for this position. Experience with social networks, disease dynamics, analysis of large data sets and with research involving human subjects is highly desirable. A PhD in life sciences or quantitative social sciences is required. Substantial domestic travel will be necessary in this position. Candidates with a multidisciplinary background, spanning the life sciences, social sciences and computer sciences, are especially encouraged to apply.

Review of applications will begin immediately. This position is available September 1, 2011. Salary and benefits are competitive.

The Center for Infectious Disease Dynamics brings together theoreticians and empirical scientists in a wide variety of disciplines to collaborate and innovate in the area of infectious disease research. In September 2011, several CIDD research groups (including ours) will move into Penn State’s new Millennium Science Complex, a building that has been designed around shared open spaces to facilitate frequent interactions among graduate students, postdoctoral researchers, and faculty working across all levels of biological complexity and methodological approaches to the study of infectious disease dynamics.

Interested applicants should submit a CV, a one page letter explicitly describing professional qualifications for this position, and contact information of three references to Marcel Salathé.

We encourage applications from individuals of diverse backgrounds. Penn State is committed to affirmative action, equal opportunity and the diversity of its workforce.