June 2015. BioJazz
We have just released a computational platform on evolving the protein-protein interaction networks, named BioJazz. In general, this program allows evolving the protein interaction networks by encoding the networks into a binary string. The mutated binary string can be translated into reaction rules that describe the interaction details as well as kinetic information. Then subsequently simulation of such reaction rules gives dynamics of the evolving networks. One can apply selection pressures (e.g. ultrasensitivity, adaptive response) on the dynamics of the network. In case you (or your students) want to check it out, please check the source code in Github: BioJazz.
June 2014. Research Programme on Microbial Communites Ready To Kick Off
About a year ago, together with several colleagues from around the UK, Denmark and New Zealand, we have received funding from the Isaac Newton Institute to organise a 4-month residential research program on "understanding microbial communities". The broad idea was to bring together empricial and theoretical scientists to discuss and develop new approaches to studying and understanding the sturcture and function of microbial communities. With this vision in our heads, we have been working on organising the program for almost a year now and the kick off is only a month away, scheduled for mid-August. Hosting well over 60 scientists over the 4-months, the research program will feature several public talks, three 3-day workshops, one student training event, and one academia/industry linking event. All aspects of the program will also be open to external participatns. If you are interested to learn more or apply for a place, please visit the program website.
May 2014. Anaerobic Digestion Network
Through our research on "engineering microbial communities for biomethane production", we got to lead development of a research/industry network on anaerobic digestion. Funded by the BBSRC, this network is now active and will be helping to develop the research on anaerobic digestion and mcirobial communities. In particular, the network will be organising several events and handing out pump prime funding. For more information and to join visit the AD Network
December 2013. UK's First Doctoral Training Centre in Synthetic Biology!
UK's first and only doctoral training centre in synthetic biology, which we have played a key role in developing and where Orkun takes an associate directorship role, is jointly funded by EPSRC and BBSRC. The centre will be known as SynBioCDT and will provide a doctoral training program that combines the fundamental understanding of biological systems with the principles of engineering, so as to create the next generation of industrial and academic leaders in synthetic biology. SynBioCDT builds on the multi-disciplinary expertise offered by the research environment at the Universities of Oxford, Bristol and Warwick to provide training that covers all parts of this extremely broad remit, including not only individual cells but self-assembled biomimetic systems, engineered microbial communities and multicellular organisms. Such coverage is vital in the emerging area of Synthetic Biology. SynBioCDT is now accepting applications from motivated students!
September 2013. University of Warwick launches Warwick Centre for Integrative Synthetic Biology!
Warwick Centre for Integrative Synthetic Biology, WISB for short, is a new interdicsiplinary centre for advancing synthetic biology research. The unique vision of WISB is to develop new engineering and experimental approaches that will facilitate improved understanding, control and exploitation of the unique features of biological systems through synthetic biology. In particular, research at WISB will focus on the role and exploitation of noise in gene circutis, evolutionarily inspired approaches to pathway engineering, and development of engineering toolkits for synthetic multi-cell, multi-compartment systems.
May 2013. OSS Lab is now part of University of Warwick, School of Life Sciences!
After three exciting and productive years at the University of Exeter, in which we played a key role in establishing systems biology approaches to biological problems, the OSS Lab has now moved to the University of Warwick, School of Life Sciences. The move sees us embarking on experimental work in our own labs and also engaging fully with the emerging field of synthetic biology. This is bound to be an exciting development for all of us at the OSS Lab, and hopefully for the larger scientific community both at Warwick and beyond.
Feb 2013. Biotechnology, Biomedicine and Microbial Communities
Most, not all, of industrial biotechnology deals with microbes in one way or the other. And when it comes to microbes the conventional thinking seem to rely on two concepts; make it simple, make it big. Thus, many industrial applications involve large reactors of clonal cultures of a single species, which usually performs some metabolic conversion. In nature, however, bacteria almost never is found in isolation but rather in heterogenous communities. Such communities are believed to kept together via structural and functional associations such as metabolic dependencies. The study of microbial communities is an emerging field, boosted by the emergence of -omics technologies. Most -omics studies are descriptive at the moment, focusing on identifying the species composition of communities. There are a plethora of other questions though. What makes a stable microbial community for example? What are the species abundance dynamics? Can one define a "function" for communities? If the function is metabolism-based, how can we understand/manipulate metabolic connections in a community? Can we de-complex natural communities? Can we create complex communities from bottom-up, starting from co-cultures? The answers to these and many other questions in microbial communities are unanswered at the moment, creating an highly fertile resaerch ground. The answers emerging from this research can make significant impact in industrial biotechnology and biomedicine.
Targeting a BBSRC call on "networks in industrial biotechnology", we are in the process of developing a research&industry network that should facilitate the "evolution" of research on microbial communities. If you want to get involved, please visit the online discussion platform BBSRC has set up for this call, or check out the outline of the idea.
Nov 2012. The Chancellor George Osborne announces our new project!
It was a big excitement for us today as the Chancellor has announced our project along with 5 others in a speech at the Royal Society. The six grants constitute a move by BBSRC towards revolutionising major industries in biotechnology and bioenergy through funding in synthetic biology. You can see the full press release by BBSRC on their web site. The grant that we're leading is on understanding natural microbial communities for biomethane production through directed evolution and engineering synthetic communities through synthetic biology. Including scientists from University of Exeter, Newcastle University, Imperial College and TGAC, this interdisciplinary project promises to make a big impact on our understanding and control of complex microbial communities. To follow our progress please keep an eye on the project web site.
Oct 2012. Metabolic Tinker.
We have just released a computational tool on "guiding" synthetic design of metabolism called Metabolic Tinker, or Tinker for short. In a nutshell, the tool allows searching the entire universe of known reactions (which we call URN :) for paths between two user given compounds. It is based on graph theory and does take into account thermodynamic feasibility of reactions. It is capable of finding both natural paths and potential alternatives, with results returned in a rank order based on total deltaG over the path. While these are novel features, Tinker is not yet the perfect design tool (e.g. it does not take into account substrate availability) but rather something that could potentially help identifying interesting solutions to a given chemical conversion problem. In case you (or your students) want to check it out, please visit the Tinker web site.
Sept 2012. Evolution in action!
As our own projects relating to better characterising microbial pathogens' behaviour and the evolution of underlying molecular systems start to mature, we were recently glued to TV to watch the beautifully made BBC documentary on evolution on antibiotic resistance. If you haven't seen it, you must catch it on the web. Among other things, it features the "morbidistat" developed in the Kishony lab and a super simple/nice experiment inspired by it. It involves growing bacteria on a large petri dish embedding a drug gradient. As bacteria grow, they evolve increasing drug resistance and leave a visible and temporally segregated colony trace on the dish. The experiment is not only a visual demonstration of evolution in action, but it also inspires several interesting follow up ideas.
July 2012. Evolutionary Systems Biology book is out!
Evolutionary Systems Biology is an emerging synthesis between evolutionary and systems
biology. I've been editing the first book on this emerging field, which is just published from Springer as part
of their Advances in Experimental Medicine and Biology series. The hope is for more such volumes to follow as the field
matures. I would like to thank again to all contributors and Melanie Tucker from Springer for a seamless publication
experience. You can order the book here
or access the individual chapters via PubMed. I hope they will provide you with thought provoking reading.
March 2012. Robustness workshop
This one day workshop organised together with Sabine Leonelli from Egenis brought together a diverse set of speakers and participants for a discussion about the role
of the engineering concepts such as robustness in biology. With the attendance of social scientists, engineers and biologists, the forum gave
rise to very interesting and fruitful discussions. The invited speakers' presentations (see poster
workshop here) provided the perfect setting
for these discussions.
January 2012. Evolution of evolvability!
The result of a long collaboration with Hiroyuki Kuwahara at Carnegie Mellon, our latest paper on the evolution of bistablity is
now online at Nature MSB web site. This has been
a most exciting and interesting work that will hopefully lead to several follow up studies both from us and others. It is exciting, because it is (I believe)
the first demonstration that systems dynamics can evolve in such a way to increase evolvability (e.g. shorten adaptation time to a new environment) of a biological system. It will be
even more exciting to see how generally applicable these results will turn out to be. This will require more theoretical and experimental work. It was interesting, because we ended up
with results that we didn't even think of at the beginning of this project. Our initial ideas were revolving around exploring the evolution of noise under fluctuating environments, but we
gradually moved to (or I should say the data pushed us to) analysing the evolution of bistability and the link of this to evolvability. In sum, it was a great journey and I'm very
glad the paper finally saw daylight!
September 2011. Introduction to systems biology and a documentary.
As part of a new MSc program
, I'm designing a new course, which will act as an introduction to systems biology. Besides discussing some of the basic tools and approaches in the field,
I would also like to use the course to make students aware of the history and philosophy of systems biology. More material from the course will be available
on this web site soon, but if you are thinking what "systems" is about, I highly recommend a recent
Adam Curtis documentary; All Watched Over By Machines of Loving Grace.
The second episode is particularly dealing with
the emergence of ideas around systems in ecology and engineering and their effects in other areas. It also provides an interesting and personal take on
how scientists/people can get carried away with their own ideas.
August 2011. Functional change in structural continuity.
A new article, co-written with my long time collaborator and previous mentor Richard Goldstein, titled "Evolution of response dynamics
underlying bacterial chemotaxis" has just come out in BMC Evolutionary Biology. I'm quite excited about this work because in it we describe a potential evolutionary
route for the response dynamics as seen in bacterial chemotaxis. This dynamics and the underlying networks have been deemed "complex" previously, but our analysis
provides a straightforward, incremental route to it at least in terms of response dynamics. Most interestingly, this route turns out to be an example for the "functional change
in structural continuity" principle first proposed by Darwin.
May 2011. Philosophy of Science.
The interest at OSS Lab into the philosophy of science and related discussions with Maureen O'Malley are slowly bearing fruit. Together, we explore in a recent publication (see publications section) how integration takes place at various levels in the general field of systems biology and how it makes an impact on knowledge generation.
The fundamental question behind this (and similar) analyses/investigations is how science as an activity differs from other forms of human activity.
March 2011. Exeter Synthetic Biology Sandpit.
Together with John Dupre (director of EGENIS), I'm organizing an internal sandpit event at the University of Exeter to increase awareness of synthetic biology research and its many facets and to foster internal collaborations in this field.
Synthetic biology aims to engineer controlled functionalities using biological systems by combining a variety of approaches and techniques from mathematics, engineering, molecular biology and genetics. Besides their clear objectives in the applied/industrial domain, such constructs are highly useful for gaining basic understanding into natural systems, allowing synthetic biology to act as a bridge between applied and basic research.
Exeter Synthetic Biology Sandpit will open with a public talk by Mark Bedau (Reed College, USA) at 6pm on 2nd June. On 3rd June, selected participants will attend a full day sandpit, with talks from four external facilitators leading into open discussion and brainstorming. Participants will interact, discuss and form research project during the day, which will be presented to facilitators and peers for feedback. We expect the emerging research projects to evolve into short proposals; those submitted by 10th June will be evaluated by a selection panel and succesful projects will be allocated a moderate sum of seed funding.
External facilitators for this event will be: Mark Bedau (Reed College); Stuart Dunbar (Syngenta); Antonis Papachristodoulou (Oxford University), Paul Freemont (Imperial College) and Jane Calvert (University of Edinburgh)
The event is sponsored by the Bridging the Gaps project, the four Colleges of the University of Exeter and the Research Knowledge Transfer unit.
January 2011. Watch top scientists present.
December 2010. Editing a book!
OSS lab head Orkun Soyer will be editing a book titled "Evolutionary Systems Biology" to be published by Springer. Evolutionary systems biology is an emerging
field that draws on systems biology, laboratory evolution, population genetics and comparative genomics to answer system level biological questions within an evolutionary
framework. To cover this broad definition the book will feature a diverse array of chapters touching on the different methodologies and approaches employed in the field
and the questions asked.
December 2010. Review process revealed.
The Publications section of this web site will from now on feature excerpts from reviews of OSS Lab publications. I decided to have this feature in an attempt to provide insight into the reviewing process, mainly as a training-experience for upcoming scientists. If you find this useful or have any other comments please get in touch. Do also get in touch if you would like to share excerpts from reviews you received.
November 2010. Varun and Al joins the lab!
OSS Lab welcomes Varun Bhaskar Kothamachu and Nihat Al Sayar, PhD. Al will explore ideas in synthetic and systems biology of metabolic networks, while Varun starts his PhD as a receipient of the prestigious Dorothy Hodgkin Award.
September 2010. Assoc. Editor at BMC!
OSS lab head Orkun Soyer is appointed as Associate Editor at BMC Evolutionary Biology, Evolutionary Systems Biology Section.
BMC Evolutionary Biology is an Open Access, peer-reviewed journal that considers articles on all aspects of molecular and non-molecular evolution of all organisms, as well as phylogenetics and palaeontology.
The journal is included in Thomson Reuters Web of Science and other products. It's latest Impact Factor is 4.29.
August 2010. Phil of Science!
OSS lab head Orkun Soyer is appointed as Senior Fellow at the ESRC Centre for Genomics in Society (Egenis). This honorary appointment acknowledges Orkun's ongoing support and contributions to research done at Egenis, in particular at the interface where public engagement, philosophy of science, systems and synthetic biology meet. For more information, visit the centre web site:
June 2010. New MSc course.
Applications are now open for an MSc program in systems biology at the University of Exeter. One of the two core modules for this program is developed by Ozgur Akman and Orkun Soyer and will focus on the Dynamics and Evolution of Biological Systems. For applications and more information, visit the course web site:
MSc Systems Biology
April 2010. A unique workshop!
Abstract submission opens for a unique workshop co-organised by Orkun Soyer. Aiming to foster interdisciplinary thought and approaches at the interface of engineering, biology and mathematics this workshop brings together leading figures and students from a variety of disciplines. For abstract submission and more information, visit the event web site:
Frontiers of multidisciplinary research: mathematics, engineering, and biology
March 2010. A good start.
OSS Lab receives two grants over the course of February and March. More details are provided in the "Funded Projects" section.