8th Annual North American School of Information Theory (NASIT)

Bookmarked 8th Annual North American School of Information Theory (NASIT) (nasit15.ucsd.edu)

August 10-13, 2015 – UC San Diego, La Jolla, California
Application deadline: June 7, 2015

The School of Information Theory will bring together over 100 graduate students, postdoctoral scholars, and leading researchers for four action-packed days of learning, stimulating discussions, professional networking and fun activities, all on the beautiful campus of the University of California, San Diego (UCSD) and in the nearby beach town of La Jolla.

  • Tutorials by some of the best known researchers in information theory and related fields
  • Poster presentations by student participants with feedback and discussion
  • Panel discussion on “IT: Academia vs. Industry Perspectives”
  • Social events and fun activities

BIRS Workshop: Advances and Challenges in Protein-RNA: Recognition, Regulation and Prediction (15w5063)

Bookmarked 15w5063: Advances and Challenges in Protein-RNA: Recognition, Regulation and Prediction (Banff International Research Station | birs.ca)
BIRS 5 day worksop, arriving in Banff, Alberta Sunday, June 7 and departing Friday, June 12, 2015

In the years since the first assembly of the human genome, the complex and vital role of RNA and RNA binding proteins in regulation of the genome expression has expanded through the discovery of RNA-binding proteins and large classes of non-coding RNA that control many developmental decisions as part of protein- RNA complexes. Our molecular level understanding of RNA regulation has dramatically improved as many new structures of RNA–protein complexes have been determined and new sophisticated experimental technologies and dedicated computational modeling have emerged to investigate these interactions at the whole-genome level. Further deep insight on the molecular mechanisms that underline genome expression regulation is critical for understanding fundamental biology and disease progression towards the discovery of new approaches to interfere with disease progression.

The proposed workshop will bring together experts in RNA biology with structural biologists that focus on RNA-protein complexes, as well as computational biologists who seek to model and develop predictive tools based on the confluence of these experimental advances. The workshop intends to foster new collaborations between experimental and computational biologists and catalyze the development of new and improved technologies (such as single cell binding methods) that merge experimental analysis with novel mathematical and computational techniques to better understand the rules of protein-RNA recognition and RNA-based biological regulation.

The organizers of the workshop are both leaders in the field of protein-RNA recognition and interactions: Yael Mandel-Gutfreund has been working in the field of protein-Nucleic Acids interactions since 1994. Her main research interest is protein-RNA recognition and regulation. She has developed several tools and web servers for predicting RNA binding proteins and RNA binding motifs. Yael is the head to the computational molecular laboratory at the Technion and the president of the Israeli society of Bioinformatics and Computational Biology. Gabriele Varani has been working in the field of RNA structure and protein-RNA interactions since 1987. His main research interest is the structural basis for protein-RNA recognition and the prediction and design of RNA-binding proteins. He determined some of the first few structures of protein-RNA complexes and developed computational tools to analyze and predict the specificity of RNA -binding proteins. His group applies these tools to design RNA-binding proteins with new specificity to control gene expression. Our invitation to participate in the workshop has been met with great enthusiasm by the researchers. More than 20 principle investigators have already confirmed their interest in attending. Six of the confirmed participants are female scientists including the organizer Yael Mandel-Gutfreund as well as Traci Hall, Lynne Maquat, Elena Conti, Susan Jones, Drena Dobbs. We also have invited and confirmed the participation of young and promising researchers including Markus Landthaler, Gene Yeo, Jernej Ule, Uwe Ohler and others. Our confirmed participants come from many different countries: US, Canada, UK, Scotland, Germany, Spain, Switzerland, Poland and Israel. Two confirmed participants as well as the organizer have attended the BIRS workshops in the past.

A key objective of the workshop is to bring together researchers with experimental, mathematical and computational background to share results and discuss the main advances and challenges in the prediction, analysis and control of RNA-protein recognition and RNA-based regulation of gene expression. Towards this aim, we plan to adopt the format of previous BIRS meetings in which invited participants (including selected students) will present relatively short presentations of 20 minutes plus 10 minutes of active discussions. This format will leave aside ample time for informal discussions to foster exchanges between participants. To stress the collaborative, multidisciplinary nature of the workshop, we plan to dedicate each of the workshop sessions to a specific topic that will comprise presentations of structural, experimental and computational approaches, rather than create session focused on a particular approach. Each session we will include at least one lecture from a young scientist/postdoctoral fellow/student to be chosen among attendees by the organizers.

Suggested preliminary schedule:

  • Day 1: Modeling and high throughput approaches to genome-wide analysis of protein-RNA interactions
  • Day 2: Predicting and designing new RNA binding proteins
  • Day 3: Generating and modeling RNA-based regulatory networks
  • Day 4: Principles of RNA regulation by RNA binding proteins
  • Day 5: Conclusion round table discussion on the present and future challenges of the field

Videos from the NIMBioS Workshop on Information and Entropy in Biological Systems

Videos from the NIMBioS workshop on Information and Entropy in Biological Systems from April 8-10, 2015 are slowly starting to appear on YouTube.

Videos from the April 8-10, 2015, NIMBioS workshop on Information and Entropy in Biological Systems are slowly starting to appear on YouTube.

John Baez, one of the organizers of the workshop, is also going through them and adding some interesting background and links on his Azimuth blog as well for those who are looking for additional details and depth

Additonal resources from the Workshop:

 

NIMBioS Workshop: Information Theory and Entropy in Biological Systems

Web resources for participants in the NIMBioS Worshop on Information Theory and Entropy in Biological Systems.

Over the next few days, I’ll be maintaining a Storify story covering information related to and coming out of the Information Theory and Entropy Workshop being sponsored by NIMBios at the Unviersity of Tennessee, Knoxville.

For those in attendance or participating by watching the live streaming video (or even watching the video after-the-fact), please feel free to use the official hashtag #entropyWS, and I’ll do my best to include your tweets, posts, and material into the story stream for future reference.

For journal articles and papers mentioned in/at the workshop, I encourage everyone to join the Mendeley.com group ITBio: Information Theory, Microbiology, Evolution, and Complexity and add them to the group’s list of papers. Think of it as a collaborative online journal club of sorts.

Those participating in the workshop are also encouraged to take a look at a growing collection of researchers and materials I maintain here. If you have materials or resources you’d like to contribute to the list, please send me an email or include them via the suggestions/submission form or include them in the comments section below.

Resources for Information Theory and Biology

RSS Icon  #ITBio" href="http://boffosocko.com/tag/ITBio/feed/" target="_blank">RSS Feed for BoffoSocko posts tagged with

 

Workshop Announcement: Entropy and Information in Biological Systems

I rarely, if ever, reblog anything here, but this particular post from John Baez’s blog Azimuth is so on-topic, that attempting to embellish it seems silly.

Entropy and Information in Biological Systems (Part 2)

John Harte, Marc Harper and I are running a workshop! Now you can apply here to attend:

Information and entropy in biological systems, National Institute for Mathematical and Biological Synthesis, Knoxville Tennesee, Wednesday-Friday, 8-10 April 2015.

Click the link, read the stuff and scroll down to “CLICK HERE” to apply. The deadline is 12 November 2014.

Financial support for travel, meals, and lodging is available for workshop attendees who need it. We will choose among the applicants and invite 10-15 of them.

The idea
Information theory and entropy methods are becoming powerful tools in biology, from the level of individual cells, to whole ecosystems, to experimental design, model-building, and the measurement of biodiversity. The aim of this investigative workshop is to synthesize different ways of applying these concepts to help systematize and unify work in biological systems. Early attempts at “grand syntheses” often misfired, but applications of information theory and entropy to specific highly focused topics in biology have been increasingly successful. In ecology, entropy maximization methods have proven successful in predicting the distribution and abundance of species. Entropy is also widely used as a measure of biodiversity. Work on the role of information in game theory has shed new light on evolution. As a population evolves, it can be seen as gaining information about its environment. The principle of maximum entropy production has emerged as a fascinating yet controversial approach to predicting the behavior of biological systems, from individual organisms to whole ecosystems. This investigative workshop will bring together top researchers from these diverse fields to share insights and methods and address some long-standing conceptual problems.

So, here are the goals of our workshop:

  •  To study the validity of the principle of Maximum Entropy Production (MEP), which states that biological systems – and indeed all open, non-equilibrium systems – act to produce entropy at the maximum rate.
  • To familiarize all the participants with applications to ecology of the MaxEnt method: choosing the probabilistic hypothesis with the highest entropy subject to the constraints of our data. We will compare MaxEnt with competing approaches and examine whether MaxEnt provides a sufficient justification for the principle of MEP.
  • To clarify relations between known characterizations of entropy, the use of entropy as a measure of biodiversity, and the use of MaxEnt methods in ecology.
  • To develop the concept of evolutionary games as “learning” processes in which information is gained over time.
  • To study the interplay between information theory and the thermodynamics of individual cells and organelles.

For more details, go here.

If you’ve got colleagues who might be interested in this, please let them know. You can download a PDF suitable for printing and putting on a bulletin board by clicking on this:

CECAM Workshop: “Entropy in Biomolecular Systems”

On Friday, I had an excellent and stimulating conversation with Arieh Ben-Naim about his recent writing and work, and he mentioned in passing that he had been invited to a conference relating to entropy and biology in Vienna.  A quick websearch found it quickly, and not having heard about it myself yet, I thought I’d pass it along to others who are regular readers and interested in the area.

The workshop on “Entropy in Biomolecular Systems” is being hosted by the Centre Européen de Calcul Atomique et Moléculaire (CECAM)

Logo for the Centre Européen de Calcul Atomique et Moléculaire (CECAM)

Location: DACAM, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9, A-1030, Vienna, Austria
Dates: May 14, 2014 to May 17, 2014

The workshop is being organized by:

  • Richard Henchman (University of Manchester, United Kingdom)
  • Bojan Zagrovic (University of Vienna, Austria)
  • Michel Cuendet (Swiss Institute of Bioinformatics, Lausanne, Switzerland and Weill Cornell Medical College, New York, USA)
  • Chris Oostenbrink (University of Natural Resources and Life Sciences, Austria)

It’s being supported by CECAM, the European Research Council, and the Royal Society of Chemistry’s Statistical Mechanics and Thermodynamics Group.

I’ll note that the registration deadline is on April 21 with a payment deadline of April 30, so check in quickly if you haven’t already.

The summary from the workshop website states:

This workshop brings together the world’s experts to address the challenges of determining the entropy of biomolecular systems, either by experiment or computer simulation. Entropy is one the main driving forces for any biological process such as binding, folding, partitioning and reacting. Our deficient understandng of entropy, however, means that such important processes remain controversial and only partially understood. Contributions of water, ions, cofactors, and biomolecular flexibility are actively examined but yet to be resolved. The state-of-the-art of each entropy method will be presented and explained, highlighting its capabilities and deficiencies. This will be followed by intensive discussion on the main areas that need improving, leading suitable actions and collaborations to address the main biological and industrial questions.

Further details on the workshop can be found on the CECAM website.

 

As always, details on other upcoming workshops and conferences relating to information theory and biology can be found on our ITBio Conferences/Workshops page.

 

 

Workshop on Information Theoretic Incentives for Artificial Life

For those interested in the topics of information theory in biology and artificial life, Christoph SalgeGeorg MartiusKeyan Ghazi-Zahedi, and Daniel Polani have announced a Satellite Workshop on Information Theoretic Incentives for Artificial Life at the 14th International Conference on the Synthesis and Simulation of Living Systems (ALife 2014) to be held at the Javits Center, New York, on July 30 or 31st.

ALife2014 Banner

Their synopsis states:

Artificial Life aims to understand the basic and generic principles of life, and demonstrate this understanding by producing life-like systems based on those principles. In recent years, with the advent of the information age, and the widespread acceptance of information technology, our view of life has changed. Ideas such as “life is information processing” or “information holds the key to understanding life” have become more common. But what can information, or more formally Information Theory, offer to Artificial Life?

One relevant area is the motivation of behaviour for artificial agents, both virtual and real. Instead of learning to perform a specific task, informational measures can be used to define concepts such as boredom, empowerment or the ability to predict one’s own future. Intrinsic motivations derived from these concepts allow us to generate behaviour, ideally from an embodied and enactive perspective, which are based on basic but generic principles. The key questions here are: “What are the important intrinsic motivations a living agent has, and what behaviour can be produced by them?”

Related to an agent’s behaviour is also the question on how and where the necessary computation to realise this behaviour is performed. Can information be used to quantify the morphological computation of an embodied agent and to what degree are the computational limitations of an agent influencing its behaviour?

Another area of interest is the guidance of artificial evolution or adaptation. Assuming it is true that an agent wants to optimise its information processing, possibly obtain as much relevant information as possible for the cheapest computational cost, then what behaviour would naturally follow from that? Can the development of social interaction or collective phenomena be motivated by an informational gradient? Furthermore, evolution itself can be seen as a process in which an agent population obtains information from the environment, which begs the question of how this can be quantified, and how systems would adapt to maximise this information?

The common theme in those different scenarios is the identification and quantification of driving forces behind evolution, learning, behaviour and other crucial processes of life, in the hope that the implementation or optimisation of these measurements will allow us to construct life-like systems.

Details for submissions, acceptances, potential talks, and dates can be found via  Nihat Ay’s Research Group on Information Theory of Cognitive Systems. For more information on how to register, please visit the ALife 2014 homepage. If there are any questions, or if you just want to indicate interest in submitting or attending, please feel free to mail them at itialife@gmail.com.

According to their release, the open access journal Entropy will sponsor the workshop by an open call with a special issue on the topic of the workshop. More details will be announced to emails received via itialife@gmail.com and over the alife and connectionists mailing lists.