A summer school for advanced undergraduates June 11-22, 2018 @ Princeton University What would it mean to have a physicist’s understanding of life? How do DYNAMICS and the EMERGENCE of ORDER affect biological function? How do organisms process INFORMATION, LEARN, ADAPT, and EVOLVE? See how physics problems emerge from thinking about developing embryos, communicating bacteria, dynamic neural networks, animal behaviors, evolution, and more. Learn how ideas and methods from statistical physics, simulation and data analysis, optics and microscopy connect to diverse biological phenomena. Explore these questions, tools, and concepts in an intense two weeks of lectures, seminars, hands-on exercises, and projects.
After hearing from a number of schools running Domain of One’s Own, we thought it might be useful to host an in-person workshop that focuses specifically on implementing this project on your campus. Workshop of One’s Own is a two-day, geared towards the instructional technologist who assists with managing DoOO on an administrator level, but also focuses on project conceptualization, instructional uses, and empowering their community from a teaching/learning standpoint. You’ll not only be receiving the in-person, focused attention from the entire Reclaim Hosting team, but you’ll also get a chance to brainstorm with folks from other schools who are running their own Domain of One’s Own projects. We’ll work through common troubleshooting tips, SPLOTs with Alan Levine, cPanel application case studies, and more.
I’m almost painfully tempted to attend this workshop on March 15-16 with the idea of and setting up a side business to specialize in hosting WordPress and Known sites for IndieWeb use. While it could be a generic non-institutional instance for academics, researchers, post docs, graduate and undergraduate students who don’t have a “home” DoOO service, it could also be a potential landing pad for those leaving other DoOO projects upon graduation or moving. Naturally I wouldn’t turn down individuals who wanted specific IndieWeb capable personal websites either.
Either way it’s an itch (at an almost poison ivy level) that I’ve been having for a long time, but haven’t written down until now. It would certainly be an interesting platform for continuing to evangelize the overlap of IndieWeb and Educational applications on the internet.
I think there are almost enough IndieWeb friendly WordPress themes to make it a worthwhile idea to have a multi-site WordPress install that has a handful of microformats performant themes in conjunction with tools like webmentions and micropub that allows easy interaction with most of the major social silos.
I think the community might almost be ready for such a platform that would allow an integrated turnkey IndieWeb experience. (Though I’d still want to offer some type of integrated feed reader experience bundled in with it.) Perhaps I could model it a little bit after edublogs and micro.blog?
Who wants to help goad me into it?
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Workshop of One’s Own: March 15 & 16 // Attendees will not only receive focused training from the entire Reclaim Hosting team, but also join in on discussion with members from other institutions running their own unique instances of Domain of One's Own // https://t.co/31NIQIRvQg pic.twitter.com/HvU8qKhQXA
— Reclaim Hosting (@ReclaimHosting) January 22, 2018
Epigenetics refers to information transmitted during cell division other than the DNA sequence per se, and it is the language that distinguishes stem cells from somatic cells, one organ from another, and even identical twins from each other. In contrast to the DNA sequence, the epigenome is relatively susceptible to modification by the environment as well as stochastic perturbations over time, adding to phenotypic diversity in the population. Despite its strong ties to the environment, epigenetics has never been well reconciled to evolutionary thinking, and in fact there is now strong evidence against the transmission of so-called “epi-alleles,” i.e. epigenetic modifications that pass through the germline.
However, genetic variants that regulate stochastic fluctuation of gene expression and phenotypes in the offspring appear to be transmitted as an epigenetic or even Lamarckian trait. Furthermore, even the normal process of cellular differentiation from a single cell to a complex organism is not understood well from a mathematical point of view. There is increasingly strong evidence that stem cells are highly heterogeneous and in fact stochasticity is necessary for pluripotency. This process appears to be tightly regulated through the epigenome in development. Moreover, in these biological contexts, “stochasticity” is hardly synonymous with “noise”, which often refers to variation which obscures a “true signal” (e.g., measurement error) or which is structural, as in physics (e.g., quantum noise). In contrast, “stochastic regulation” refers to purposeful, programmed variation; the fluctuations are random but there is no true signal to mask.
This workshop will serve as a forum for scientists and engineers with an interest in computational biology to explore the role of stochasticity in regulation, development and evolution, and its epigenetic basis. Just as thinking about stochasticity was transformative in physics and in some areas of biology, it promises to fundamentally transform modern genetics and help to explain phase transitions such as differentiation and cancer.
This workshop will include a poster session; a request for poster titles will be sent to registered participants in advance of the workshop.
Adam Arkin (Lawrence Berkeley Laboratory)
Gábor Balázsi (SUNY Stony Brook)
Domitilla Del Vecchio (Massachusetts Institute of Technology)
Michael Elowitz (California Institute of Technology)
Andrew Feinberg (Johns Hopkins University)
Don Geman (Johns Hopkins University)
Anita Göndör (Karolinska Institutet)
John Goutsias (Johns Hopkins University)
Garrett Jenkinson (Johns Hopkins University)
Andre Levchenko (Yale University)
Olgica Milenkovic (University of Illinois)
Johan Paulsson (Harvard University)
Leor Weinberger (University of California, San Francisco (UCSF))
The equations of gauge theory lie at the heart of our understanding of particle physics. The Standard Model, which describes the electromagnetic, weak, and strong forces, is based on the Yang-Mills equations. Starting with the work of Donaldson in the 1980s, gauge theory has also been successfully applied in other areas of pure mathematics, such as low dimensional topology, symplectic geometry, and algebraic geometry.
More recently, Witten proposed a gauge-theoretic interpretation of Khovanov homology, a knot invariant whose origins lie in representation theory. Khovanov homology is a “categorification” of the celebrated Jones polynomial, in the sense that its Euler characteristic recovers this polynomial. At the moment, Khovanov homology is only defined for knots in the three-sphere, but Witten’s proposal holds the promise of generalizations to other three-manifolds, and perhaps of producing new invariants of four-manifolds.
This workshop will bring together researchers from several different fields (theoretical physics, mathematical gauge theory, topology, analysis / PDE, representation theory, symplectic geometry, and algebraic geometry), and thus help facilitate connections between these areas. The common focus will be to understand Khovanov homology and related invariants through the lens of gauge theory.
This workshop will include a poster session; a request for posters will be sent to registered participants in advance of the workshop.
Edward Witten will be giving two public lectures as part of the Green Family Lecture series:
March 6, 2017
From Gauge Theory to Khovanov Homology Via Floer Theory
The goal of the lecture is to describe a gauge theory approach to Khovanov homology of knots, in particular, to motivate the relevant gauge theory equations in a way that does not require too much physics background. I will give a gauge theory perspective on the construction of singly-graded Khovanov homology by Abouzaid and Smith.
March 8, 2017
An Introduction to the SYK Model
The Sachdev-Ye model was originally a model of quantum spin liquids that was introduced in the mid-1990′s. In recent years, it has been reinterpreted by Kitaev as a model of quantum chaos and black holes. This lecture will be primarily a gentle introduction to the SYK model, though I will also describe a few more recent results.
The Santa Fe Institute, in New Mexico, is a place for studying complex systems. I’ve never been there! Next week I’ll go there to give a colloquium on network theory, and also to participate in this workshop.
I just found out about this from John Carlos Baez and wish I could go! How have I not managed to have heard about it?
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November 16, 2016 – November 18, 2016
Noyce Conference Room
This workshop will address a fundamental question in theoretical biology: Does the relationship between statistical physics and the need of biological systems to process information underpin some of their deepest features? It recognizes that a core feature of biological systems is that they acquire, store and process information (i.e., perform computation). However to manipulate information in this way they require a steady flux of free energy from their environments. These two, inter-related attributes of biological systems are often taken for granted; they are not part of standard analyses of either the homeostasis or the evolution of biological systems. In this workshop we aim to fill in this major gap in our understanding of biological systems, by gaining deeper insight in the relation between the need for biological systems to process information and the free energy they need to pay for that processing.
The goal of this workshop is to address these issues by focusing on a set three specific question:
- How has the fraction of free energy flux on earth that is used by biological computation changed with time?;
- What is the free energy cost of biological computation / function?;
- What is the free energy cost of the evolution of biological computation / function.
In all of these cases we are interested in the fundamental limits that the laws of physics impose on various aspects of living systems as expressed by these three questions.
Purpose: Research Collaboration
SFI Host: David Krakauer, Michael Lachmann, Manfred Laubichler, Peter Stadler, and David Wolpert
Live Tweeting and Twitter Lists
While attending the upcoming conference Dodging the Memory Hole 2016: Saving Online News later this week, I’ll make an attempt to live Tweet as much as possible. (If you’re following me on Twitter on Thursday and Friday and find me too noisy, try using QuietTime.xyz to mute me on Twitter temporarily.) I’ll be using Kevin Marks‘ excellent Noter Live web app to both send out the tweets as well as to store and archive them here on this site thereafter (kind of like my own version of Storify.)
In getting ramped up to live Tweet it, it helps significantly to have a pre-existing list of attendees (and remote participants) talking about #DtMH2016 on Twitter, so I started creating a Twitter list by hand. I realized that it would be nice to have a little bot to catch others as the week progresses. Ever lazy, I turned to IFTTT.com to see if something already existed, and sure enough there’s a Twitter search with a trigger that will allow one to add people who mention a particular hashtag to a Twitter list automatically.
Here’s the resultant list, which should grow as the event unfolds throughout the week:
🔖 People on Twitter talking about #DtMH2016
Feel free to follow or subscribe to the list as necessary. Hopefully this will make attending the conference more fruitful for those there live as well as remote.
Not on the list? Just tweet a (non-private) message with the conference hashtag: #DTMH2016 and you should be added to the list shortly.
IFTTT Recipe for Creating Twitter Lists of Conference Attendees
For those interested in creating their own Twitter lists for future conferences (and honestly the hosts of all conferences should do this as they set up their conference hashtag and announce the conference), below is a link to the ifttt.com recipe I created for this, but which can be modified for use by others.
Naturally, it would also be nice if, as people registered for conferences, they were asked for their Twitter handles and websites so that the information could be used to create such online lists to help create longer lasting relationships both during the event and afterwards as well. (Naturally providing these details should be optional so that people who wish to maintain their privacy could do so.)Syndicated copies to:
Methods originally developed in Information Theory have found wide applicability in computational neuroscience. Beyond these original methods there is a need to develop novel tools and approaches that are driven by problems arising in neuroscience. A number of researchers in computational/systems neuroscience and in information/communication theory are investigating problems of information representation and processing. While the goals are often the same, these researchers bring different perspectives and points of view to a common set of neuroscience problems. Often they participate in different fora and their interaction is limited. The goal of the workshop is to bring some of these researchers together to discuss challenges posed by neuroscience and to exchange ideas and present their latest work. The workshop is targeted towards computational and systems neuroscientists with interest in methods of information theory as well as information/communication theorists with interest in neuroscience.
A BIRS / Casa Matemática Oaxaca Workshop arriving in Oaxaca, Mexico Sunday, July 31 and departing Friday August 5, 2016
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Evolutionary biology is a rapidly changing field, confronted to many societal problems of increasing importance: impact of global changes, emerging epidemics, antibiotic resistant bacteria… As a consequence, a number of new problematics have appeared over the last decade, challenging the existing mathematical models. There exists thus a demand in the biology community for new mathematical models allowing a qualitative or quantitative description of complex evolution problems. In particular, in the societal problems mentioned above, evolution is often interacting with phenomena of a different nature: interaction with other organisms, spatial dynamics, age structure, invasion processes, time/space heterogeneous environment… The development of mathematical models able to deal with those complex interactions is an ambitious task. Evolutionary biology is interested in the evolution of species. This process is a combination of several phenomena, some occurring at the individual level (e.g. mutations), others at the level of the entire population (competition for resources), often consisting of a very large number of individuals. the presence of very different scales is indeed at the core of theoretical evolutionary biology, and at the origin of many of the difficulties that biologists are facing. The development of new mathematical models thus requires a joint work of three different communities of researchers: specialists of partial differential equations, specialists of probability theory, and theoretical biologists. The goal of this workshop is to gather researchers from each of these communities, currently working on close problematics. Those communities have usually few interactions, and this meeting would give them the opportunity to discuss and work around a few biological thematics that are especially challenging mathematically, and play a crucial role for biological applications.
The role of a spatial structure in models for evolution: The introduction of a spatial structure in evolutionary biology models is often challenging. It is however well known that local adaptation is frequent in nature: field data show that the phenotypes of a given species change considerably across its range. The spatial dynamics of a population can also have a deep impact on its evolution. Assessing e.g. the impact of global changes on species requires the development of robust mathematical models for spatially structured populations.
The first type of models used by theoretical biologists for this type of problems are IBM (Individual Based Models), which describe the evolution of a finite number of individuals, characterized by their position and a phenotype. The mathematical analysis of IBM in spatially homogeneous situations has provided several methods that have been successful in the theoretical biology community (see the theory of Adaptive Dynamics). On the contrary, very few results exist so far on the qualitative properties of such models for spatially structured populations.
The second class of mathematical approach for this type of problem is based on ”infinite dimensional” reaction-diffusion: the population is structured by a continuous phenotypic trait, that affects its ability to disperse (diffusion), or to reproduce (reaction). This type of model can be obtained as a large population limit of IBM. The main difficulty of these models (in the simpler case of asexual populations) is the term modeling the competition from resources, that appears as a non local competition term. This term prevents the use of classical reaction diffusion tools such as the comparison principle and sliding methods. Recently, promising progress has been made, based on tools from elliptic equations and/or Hamilton-Jacobi equations. The effects of small populations can however not be observed on such models. The extension of these models and methods to include these effects will be discussed during the workshop.
Eco-evolution models for sexual populations:An essential question already stated by Darwin and Fisher and which stays for the moment without answer (although it continues to intrigue the evolutionary biologists) is: ”Why does sexual reproduction maintain?” Indeed this reproduction way is very costly since it implies a large number of gametes, the mating and the choice of a compatible partner. During the meiosis phasis, half of the genetical information is lost. Moreover, the males have to be fed and during the sexual mating, individual are easy preys for predators. A partial answer is that recombination plays a main role by better eliminating the deleterious mutations and by increasing the diversity. Nevertheless, this theory is not completely satisfying and many researches are devoted to understanding evolution of sexual populations and comparison between asexual and sexual reproduction. Several models exist to model the influence of sexual reproduction on evolving species. The difficulty compared to asexual populations is that a detailed description of the genetic basis of phenotypes is required, and in particular include recombinations. For sexual populations, recombination plays a main role and it is essential to understand. All models require strong biological simplifications, the development of relevant mathematical methods for such mechanisms then requires a joint work of mathematicians and biologists. This workshop will be an opportunity to set up such collaborations.
The first type of model considers a small number of diploid loci (typically one locus and two alleles), while the rest of the genome is considered as fixed. One can then define the fitness of every combination of alleles. While allowing the modeling of specific sexual effects (such as dominant/recessive alleles), this approach neglects the rest of the genome (and it is known that phenotypes are typically influenced by a large number of loci). An opposite approach is to consider a large number of loci, each locus having a small and additive impact on the considered phenotype. This approach then neglects many microscopic phenomena (epistasis, dominant/recessive alleles…), but allows the derivation of a deterministic model, called the infinitesimal model, in the case of a large population. The construction of a good mathematical framework for intermediate situation would be an important step forward.
The evolution of recombination and sex is very sensitive to the interaction between several evolutionary forces (selection, migration, genetic drift…). Modeling these interactions is particularly challenging and our understanding of the recombination evolution is often limited by strong assumptions regarding demography, the relative strength of these different evolutionary forces, the lack of spatial structure… The development of a more general theoretical framework based on new mathematical developments would be particularly valuable.
Another problem, that has received little attention so far and is worth addressing, is the modeling of the genetic material exchanges in asexual population. This phenomena is frequent in micro-organisms : horizontal gene transfers in bacteria, reassortment or recombination in viruses. These phenomena share some features with sexual reproduction. It would be interesting to see if the effect of this phenomena can be seen as a perturbation of existing asexual models. This would in particular be interesting in spatially structured populations (e.g. viral epidemics), since the the mathematical analysis of spatially structured asexual populations is improving rapidly.
Modeling in evolutionary epidemiology: Mathematical epidemiology has been developing since more than a century ago. Yet, the integration of population genetics phenomena to epidemiology is relatively recent. Microbial pathogens (bacteria and viruses) are particularly interesting organisms because their short generation times and large mutation rates allow them to adapt relatively fast to changing environments. As a consequence, ecological (demography) and evolutionary (population genetics) processes often occur at the same pace. This raises many interesting problems.
A first challenge is the modeling of the spatial dynamics of an epidemics. The parasites can evolve during the epidemics of a new host population, either to adapt to a heterogeneous environment, or because it will itself modify the environment as it invades. The applications of such studies are numerous: antibiotic management, agriculture… An aspect of this problem for which our workshop can bring a significant contribution (thanks to the diversity of its participants) is the evolution of the pathogen diversity. During the large expansion produced by an epidemics, there is a loss of diversity in the invading parasites, since most pathogens originate from a few parents. The development of mathematical models for those phenomena is challenging: only a small number of pathogens are present ahead of the epidemic front, while the number of parasites rapidly become very large after the infection. The interaction between a stochastic micro scale and a deterministic macro scale is apparent here, and deserves a rigorous mathematical analysis.
Another interesting phenomena is the effect of a sudden change of the environment on a population of pathogens. Examples of such situations are for instance the antibiotic treatment of an infected patients, or the transmission of a parasite to a new host species (transmission of the avian influenza to human beings, for instance). Related experiments are relatively easy to perform, and called evolutionary rescue experiments. So far, this question has received limited attention from the mathematical community. The key is to estimate the probability that a mutant well adapted to the new environment existed in the original population, or will appear soon after the environmental change. Interactions between biologists specialists of those questions and mathematicians should lead to new mathematical problems.
For the first time since 2013, when it appeared in Hollywood, IndieWebCamp is coming to Los Angeles! I’m definitely going, and I invite you to join us. For the past two years or so, I’ve been delving into the wealth of tools and resources the community has been developing. I’m excited to attend a local camp, help out in any way I can, and will help anyone who’s interested in learning more.
Join us in LA (Santa Monica) for two days of a BarCamp-style gathering of web creators building and sharing open web technologies to empower users to own their own identities & content, and advance the state of the #indieweb!
The IndieWeb movement is a global community that is building an open set of principles and methods that empower people to take back ownership of their identity and data instead of relying on 3rd party websites.
At IndieWebCamp you’ll learn about ways to empower yourself to own your data, create & publish content on your own site, and only optionally syndicate to third-party silos. Along the way you’ll get a solid grounding in the history and future of Microformats, domain ownership, IndieAuth, WebMention and more!
For remote participants, tune into the live chat (tons of realtime notes!) and the video livestream (URL TBD).
General IndieWeb Principles
|Your content is yours
When you post something on the web, it should belong to you, not a corporation. Too many companies have gone out of business and lost all of their users’ data. By joining the IndieWeb, your content stays yours and in your control.
|You are better connected
Your articles and status messages can go to all services, not just one, allowing you to engage with everyone. Even replies and likes on other services can come back to your site so they’re all in one place.
|You are in control
You can post anything you want, in any format you want, with no one monitoring you. In addition, you share simple readable links such as example.com/ideas. These links are permanent and will always work.
Friday (optional): 2016-11-04
Day 0 Prep Night
Day 0 is an optional prep night for people that want to button up their website a little bit to get ready for the IndieWebCamp proper.
18:30 Organizer setup
19:00 Doors open
19:30 Build session
22:00 Day 0 closed
Day 1 Discussion
Day 1 is about discussing in a BarCamp-like environment. Bring a topic you’d like to discuss or join in on topics as they are added to the board. We make the schedule together!
08:00 Organizer setup
08:30 Doors open – badges
09:15 Introductions and demos
10:00 Session scheduling
12:00 Group photo & Lunch
13:00 Sessions on the hour
16:00 Last session
17:00 Day 1 closing session, break, meetup later for dinner
Day 2 Building
Day 2 is about making things on and for your personal site! Work with others or on your own.
09:30 Doors open – badges
10:10 Day 2 kick-off, session scheduling
10:30 Build sessions
12:00 Catered lunch
14:30 Build sessions continue
16:30 Community clean-up
17:00 Camp closed!
Sponsorship opportunities are available for those interested.Syndicated copies to:
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The 2016 School of information will be hosted at Duke University, June 21-23. It is sponsored by the IEEE Information Theory Society, Duke University, the Center for Science of Information, and the National Science Foundation. The school provides a venue where doctoral and postdoctoral students can learn from distinguished professors in information theory, meet with fellow researchers, and form collaborations.
Program and Lectures
The daily schedule will consist of morning and afternoon lectures separated by a lunch break with poster sessions. Students from all research areas are welcome to attend and present their own research via a poster during the school. The school will host lectures on core areas of information theory and interdisciplinary topics. The following lecturers are confirmed:
- Helmut Bölcskei (ETH Zurich): The Mathematics of Deep Learning
- Natasha Devroye (University of Illinois, Chicago): The Interference Channel
- René Vidal (Johns Hopkins University): Global Optimality in Deep Learning and Beyond
- Tsachy Weissman (Stanford University): Information Processing under Logarithmic Loss
- Aylin Yener (Pennsylvania State University): Information-Theoretic Security
Applications will be available on March 15 and will be evaluated starting April 1. Accepted students must register by May 15, 2016. The registration fee of $200 will include food and 3 nights accommodation in a single-occupancy room. We suggest that attendees fly into the Raleigh-Durham (RDU) airport located about 30 minutes from the Duke campus. Housing will be available for check-in on the afternoon of June 20th. The main part of the program will conclude after lunch on June 23rd so that attendees can fly home that evening.
Administrative Contact: Kathy Peterson, firstname.lastname@example.org
Henry Pfister (chair) (Duke University), Dror Baron (North Carolina State University), Matthieu Bloch (Georgia Tech), Rob Calderbank (Duke University), Galen Reeves (Duke University). Advisors: Gerhard Kramer (Technical University of Munich) and Andrea Goldsmith (Stanford)
August 10-13, 2015 – UC San Diego, La Jolla, California
Application deadline: June 7, 2015
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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 5 day worksop, arriving in Banff, Alberta Sunday, June 7 and departing Friday, June 12, 2015
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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
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 page
- Participants list
- Workshop Agenda [.pdf download]
- Information and Entropy WordPress site
- YouTube playlist of videos
- Storify archive from the workshop
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.
- References and Journal Articles
- Related Academic, Research Institutes, Societies, Groups, and Organizations
- Conferences, Workshops, and Symposia
- Bionet.Info-Theory (Google Group/Usenet Group)
- #ITBio on Twitter
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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)
• 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.
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: