10th International Conference on Information Processing in Cells and Tissues
IPCAT 2015, San Diego, USA, 14th-16th September 2015

Updates:

Celebrating the 20th anniversary of the IPCAT conference series, IPCAT 2015 aims to bring together researchers from the biological, physical, computational and mathematical sciences who have a common interest in the nature of biological information processing. We welcome both those who are interested in understanding biological systems and those who are interested in applying biological principles within artificial systems. This year's conference will take place in the biomedical hub city of San Diego, California.

Examples of topics addressed at previous IPCAT conferences include:

  • Synthetic, executable and computational biology
  • Natural computation and artificial life
  • Computational intelligence and machine learning
  • Neural modelling and neural computing
  • Evolvable and adaptive hardware
  • Evolutionary and biochemical robotics
  • Artificial tissues and organs
  • Molecular evolution and theoretical biology
  • Artificial biosensor and vision implementations
  • Quantum computation in cells and tissues
  • Modeling of metabolic pathways and responses
  • Developmental and morphogenetic systems
  • Simulation of genetic and ecological systems
  • Biological applications of nanotechnology
  • DNA, chemical and bacterial computing
  • Systems biology and bioinformatics
  • Genome biology and mathematical biology
  • Biomedical engineering and clinical informatics

The conference proceedings will be published in Springer's LNCS series, and selected papers will be included in a special issue of the journal BioSystems.

History of the IPCAT series



The IPCAT series of conferences began in 1995 as a venue to bring together a group of multidisciplinary scientists interested in modelling the processes that take place within biological cells and tissues. Over the years, the conference has been organised by biologists, mathematicians, computer scientists and electronic engineers, but has always aimed to attract a diverse and multidisciplinary group of delegates. As noted by Ray Paton and Mike Holcombe in the forward to the first IPCAT workshop, "one of the key motivations underlying the first IPCAT Workshop was to attempt to provide a common ground for dialogue and reporting research without emphasising one particular research constituency or way of modelling or singular issue in this area."

The topics addressed at IPCAT significantly overlap with the remit of the long-running journal BioSystems, and since 1999 selected papers have been published as a special issue. Starting with IPCAT 2012, and reflecting the increasing overlap between biology and computer science, submissions to IPCAT have also been published in Springer's Lecture Notes in Computer Science series.

Previous events in the IPCAT series were:

Note these are not the instructions for the camera ready version. Please click on the "Camera Ready" tab for this.

All submissions should be in PDF format using the IPCAT 2015 EasyChair submission system. If you do not already have an EasyChair account, please register. No email submissions will be accepted.

Recognising the different publishing expectations of different communities, we accept sumission of both full papers and extended abstracts. Submissions should describe recent research that has not been published elsewhere.

Full papers
Full papers should adhere to the LNCS format, and may be up to 12 pages in length including all figures, tables and references. See the Springer LNCS Author Guidelines for formatting instructions. All accepted full papers will be published in the LNCS proceedings.

Extended abstracts
Extended abstracts may be up to 3 A4 pages in length (minimum 10pt text) and may include figures and tables as appropriate. Accepted abstracts will be distributed to conference delegates and be made available via the conference website. Authors will also have the opportunity to submit a short paper for publication in the LNCS proceedings.

Late breaking papers
If you would like to present at the late breaking papers session, please email a one page abstract to the programme chair, Michael Lones, at M.Lones@hw.ac.uk by August 21st. Title your email "IPCAT late breaking paper session".

BioSystems Special Issue
All submissions will be considered for extended versions in the special issue of BioSystems. Decisions will be made after the conference has taken place.

All submissions will undergo peer review. By submitting, at least one of the authors agrees to register for and participate in IPCAT 2015 if the submission is accepted.

Key Dates
Submission deadline: 23rd March 2015 20th April 2015
Acceptance notification: 18th May 2015 22nd May 2015 25th May 2015
Final copy deadline: 1st June 2015 12th June 2015

The camera-ready version of your paper is due by 12th June 2015. Please take into account the reviewers' comments when preparing the final version of your submission and remember that there is a page limit of 20 single-side pages for full papers and 10 single-side pages for short papers, both formatted according to Springer's LNCS formatting instructions. Both LaTeX and MS Word templates are available from Springer.

Camera ready submissions should be emailed to the programme chair, Michael Lones, at M.Lones@hw.ac.uk. Title your email "IPCAT camera ready". Please send a single compressed archive (either zip or gzip) containing a single directory. The archive should be called 'NameID.zip' (or .tgz) where 'Name' is the surname of the first author, and 'ID' is the Paper ID allocated to your submission by EasyChair. The directory, titled 'NameID' should contain the following files:

  1. The final PDF version of your submission, called 'NameID.pdf'.
  2. All source files for your submission:
    • For submissions prepared in LaTeX2e, this should include all .tex files, all image files (.ps, .eps, .pdf, .jpg), and bibliography files (.bib, .bbl).
    • For submissions prepared in MS Word or similar, this should include a .doc file (with figures) and also separate files for each image (.ps, .eps, .pdf, .jpg).
  3. An ASCII text file called 'authors.txt' containing the names and email addresses of the corresponding authors (one author per line, in the format: 'first name' 'last name' 'email address'). Please mark the corresponding author with an asterisk ('*') at the end of the line.
  4. An ASCII text file called 'abstract.txt' containing the title and abstract of your submission.
  5. A signed and scanned PDF of the Springer LNCS Copyright Form, named 'NameIDcr.pdf'. This should be signed by at least one of the authors and contain the following information in the first two fields:
    • The 'Title of the Book or Conference Name' field should contain '10th International Conference on Information Processing in Cells and Tissues'
    • The 'Volume Editor(s)' field should contain 'G. Fogel, M. A. Lones, S.L. Smith and A.M. Tyrrell'

Also remember that at least one author for each submission must register for the conference no later than 30th June 2015. Registration instructions will appear soon.

Registration and Hotel Reservations

Registration for whole conference: $585
Single day registration (conference dinner not included): $165
Extra conference dinner ticket: $120

Click here to go to the registration site.

Registration fee includes admission to all keynote talks and technical sessions. Price also includes morning and afternoon tea/coffee breaks (including hot and cold drinks, and a selection of muffins, fruit and cakes), lunch each day (3-course meal), one ticket for the conference banquet (3-course meal including wine and soft drinks),and receptions (drinks and nibbles) on Sunday and Monday nights. Registration also covers one copy of the proceedings and one accepted paper (all papers require one registration to be included in the proceedings and to be considered for the Special Issue of the BioSystems journal).

Hotel Reservations


We have obtained an excellent rate for rooms at the conference hotel (Embassy Suites San Diego Bay – Downtown) of $159 per night (this covers 13th-17th September, but book early and this rate could well extend to further dates).

Booking rooms is simple and requires no up-front payments, simply go to the IPCAT hotel web page.

The Group name for our event is: "Information Processing in Cells and Tissues" and the Group Code is "PCT".

As well as being the conference hotel, the location and rooms are excellent and we encourage you to book early as rooms at this special rate are limited and the offer only lasts until 15th August, so book now!

Speakers will be added as details become available.

Lee Altenberg“How might evolutionary theory inform research on information processing in cells and tissues?”
Abstract
The ability of organisms to gather information from their environment and act on it appropriately for survival, as well as to process information in creating their physiology, remain unmatched by artificial systems. In some cases, like the lac operon, the systems are understandable from a design perspective, while in other cases, like the mammalian immune system, the `principles' of their operation are difficult to understand. One might hope that some understanding could be drawn from the larger processes that give rise to this information processing - ecological and Darwinian dynamics. Here, I focus on several sets of questions: First, how does evolution ever produce understandable systems? The process of "constructive neutral evolution" (Stoltzfus) can lead to uselessly complex organismal organization. Second, to what degree are the information processing systems we see explained by their function, or are rather shaped to provide mutational or recombinational robustness and evolvability? Lastly, how might the nature of evolved systems collide with our standard research paradigms of modeling, hypothesis testing, theory building, and attempts to control through engineering?
Dr. Altenberg is a Senior Fellow at The KLI, Klosterneuburg Austria, and is an evolutionary theoretician, focusing on the evolution of variation production in organisms (including genetic systems, evolvability, modularity and the genotype-phenotype map) and evolutionary computation.
Kwang-Hyun Cho“Unraveling the Information Processing Machinery Within a Living Cell”
Abstract
Cells encounter various environmental changes during their life and, to survive, they must make right decisions and cope with such changes. So, cells might have evolved a sort of information processing machinery that senses external inputs and actuates right responses. What is this machinery and how does it work? There are increasing evidences on the complexity of cellular signaling networks and the possibility of their information processing capability. Systems biology is a new interdisciplinary science between systems science and biology that can provide a useful framework for exploring such questions. Systems biology involves the study of complex biomolecular interaction networks through mathematical modeling, computer simulation and biological experimentation. The eventual goal of systems biology is to unravel a hidden design principle underlying complex biological phenomena and to find a way to control the biological process as we want. In this talk, I will introduce the main concept of systems biology through several illustrative case studies ranging from a small scale signal transduction pathway to a large and complex molecular interaction network and discuss the perspectives of systems biology with a particular focus on untangling complex biomolecular interaction networks to expound the information processing capability of a cellular system.
Dr. Kwang-Hyun Cho is a KAIST-Chair Professor in the Department of Bio and Brain Engineering at the Korea Advanced Institute of Science and Technology (KAIST) and has been working on systems biology and bio-inspired engineering. His innovative contribution to these areas by combining physical modeling, biological experimentation, and engineering implementation has led to over 130 high-profile international journal publications. He is the founding Editor-in-Chief of IET Systems Biology (IET, London).
Terry Gaasterland“Genome variation in regulatory regions and impact on human diseases: a case study in optic nerve degeneration”
Abstract
In glaucoma, progressive optic nerve degeneration can lead to irreversible vision impairment and eventual blindness, despite treatment. Genetic causes and influences are not yet clear in primary open angle glaucoma (POAG), the most prevalent form of the disease in North America, Europe, and several other parts of the world. The genetics of POAG are complex; to date, no single causative genomic variant has been established as causing the disease.
Genome-wide sequencing of exons from protein coding and non-coding genes in 295 patients with primary open angle glaucoma revealed over 50 associated SNP sites within over 30 genes. Of these, two-thirds were located in introns or untranslated regions (UTR). To rank and prioritize genes and generate hypotheses about molecular mechanisms disrupted by associated variant sites, mRNA and small RNA (microRNA) were sequenced from ocular tissues relevant to the disease. Intronic SNPs were assessed for impact on alternative splice isoforms, and UTR SNPs were assessed for impact on microRNA binding. An additional cohort of associated SNPs appear between genes and in follow-up analysis may implicate enhancers or promoters in disease processes.
Analysis protocols and techniques for integrated data interpretation to construct putative regulatory networks underlying disease will be discussed. The approach revealed two strong candidate models explaining neurodegeneration in POAG. The data collection and analysis methods are generally applicable beyond glaucoma to other chronic, progressive diseases associated with aging.
Dr. Gaasterland is Professor of Computational Biology and Genomics at the University of California, San Diego, with appointments at UCSD's Scripps Institution of Oceanography, the Institute for Genomic Medicine, and the Program in Bioinformatics and Systems Biology.
Marco Salemi“Phylodynamic analysis of viral and bacterial pathogens in the genomics era”
Abstract
Phylogenetic inference from molecular sequences is a powerful tool to trace the patterns of inter- and intra-host pathogen evolution, as well as geographic dispersal (molecular epidemiology). During the past decade, a new framework has been developed, called phylodynamics that combines phylogenetic analysis and coalescence theory to correlate the epidemiology and evolutionary behavior of pathogens. The time-scale of epidemic spread usually provides ample time for evolving pathogens to accumulate informative mutations in their genomes. Reconstructing both the evolutionary history from viral sequences, for example, has provided a fundamental understanding of the evolutionary dynamics underlying epidemics of viruses such as HIV, HCV and Ebola. By using a statistical model, known as the relaxed molecular clock, it is possible to infer the genealogy and evolutionary time-scale of the sampled sequences. Spatial diffusion also leaves a measurable footprint in sampled gene sequences and Bayesian phylogeography can successfully be used to reconstruct the gene flow (migration/spread) of pathogens and test hypotheses of spatial spread. Such studies have been used, for example, to reconstruct in detail the emergence and dissemination of HIV-1 in the African continent. More recently, phylodynamic analysis has been applied to the study of bacterial infections. The emerging field of genomic epidemiology, based on the analysis of full genome next generation sequences, can help understanding the spread of bacterial pathogens, such as methicillin-resistant staphylococcus aureus (MRSA) and Vibrio cholerae, and provide fundamental information for the development of prevention strategies, vaccines, and even novel therapeutic targets.
Dr. Marco Salemi, PhD is Associate Professor at the Department of Pathology, Immunology and Laboratory Medicine of the University of Florida (UF) College of Medicine and the director of the phylodynamics lab at the UF Emerging Pathogens Institute. He is an internationally recognized expert in the area of phylogenetic analysis and molecular evolution of human and animal pathogens.
Anthony Newman“How to Write a Great Research Paper, and Get it Accepted by a Good Journal” Slides: Part1 Part2
Abstract
Background: Knowing the best way of structuring your paper when writing it, and the most appropriate journal to send it to, really helps in getting your paper accepted. Also understanding how editors and publishers think and what they expect, and knowing how the peer review process works, is invaluable insight into the publishing process.
Results: After attending this free 1 hour workshop, one in the Elsevier Publishing Connect Workshop series, participants will have a clear idea of the steps needed to be taken before starting to write a paper. They will also be able to plan writing manuscripts using the logical step sequence – not the sequence in which the paper will be read. Authors are also made aware of what aspects of their papers Editors and Publishers look at critically, and to ensure that in taking care of these areas, their papers are much more likely to be accepted. Dealing with referees’ comments and the art of polite rebuttal are also described such that these can be used to improve the submitted paper suitably. Sensitive areas such as publishing ethics, plagiarism, duplicate publishing, etc are also clearly explained such that participants have a clear understanding of what their responsibilities are, what is allowed, and what is not permitted.
For senior researchers this is an opportunity to learn a structured approach to scientific authorship, which you can pass on to your students and junior faculty.
Conclusions: These insights into the publishing process will enable the participants to be more confident as an author in the world of science publishing, and so should help them get their papers published more easily.
Anthony Newman is a Senior Publisher with Elsevier, and is based in Amsterdam. Currently responsible for several laboratory medicine and biochemistry journals, he joined Elsevier 28 years ago and has been Publisher for the last 15 years. Before then he was the marketing communications manager for the biochemistry journals of Elsevier. By training he is a polymer chemist and was active in industry before leaving London and moving to Amsterdam in 1987 to join Elsevier.

Embassy Suites, San Diego Bay, Downtown

The conference will be held in the Embassy Suites, located beside the beautiful San Diego Bay, and near to the city's historic centre.

San Diego

San Diego, the historic birthplace of California, is nowadays known for its colonial era architecture, its pleasant year round climate, and as a hub for the healthcare and biotechnology industries. Many attractions can be found within walking distance of the Embassy Suites, including:

Aircraft Carrier USS Midway. Commissioned a week after the end of World War II, the Midway was the largest ship in the world until 1955, seeing action in the Vietnam War and in 1991's Operation Desert Storm.

Maritime Museum of San Diego, whose collection includes the world's oldest sailing ship, HMS Surprise from the film "Master and Commander", and a B-39 soviet-era Russian attack submarine.

The Museum of Contemporary Art which showcases an internationally recognised collection of contemporary art in a historic setting.

The Headquarters speciality shops, restaurants and entertainment venues, including the award-winning Seasons 52 grill and wine bar and Puesto, known for its refined Mexican street food.

Many other attractions are accessible via taxi or public transport, including the famous San Diego Zoo, San Diego Air and Space Museum, San Diego History Center and Sea World.

Travelling by Air

San Diego International Airport is less than 10 minutes from downtown San Diego. Direct international connections are available to London, Tokyo, Mexico and Canada. Other international destinations are served via changes at Los Angeles and San Francisco.

Taxis to downtown cost approximately $15-20. Other transfer options include airport shuttles, Metro bus 992, Uber and Lyft. It is also possible to walk.

Travelling by Rail

Amtrak's Pacific Surfliner route provides connections to Los Angeles, Santa Barbara, and San Luis Obispo. The station is within walking distance of downtown hotels and situated near San Diego Bay.

Organising Committee

General Chairs
Prof. Andy Tyrrell, Electronics, University of York, UK
Dr. Stephen Smith, Electronics, University of York, UK

Local Chair
Dr. Gary Fogel, Natural Selection Inc., USA

Programme Chair
Dr. Michael Lones, Mathematical and Computer Sciences, Heriot-Watt University, UK

Programme Committee
Alexander Bockmayr, Mathematics, Freie Universitat Berlin, Germany
Rachel Cavill, Toxicogenomics, Maastricht University, Netherlands
Jerry Chandler, Krasnow Institute, George Mason University, USA
Ron Cottam, Electronics and Informatics, Vrije Universiteit Brussel, Belgium
Peter Erdi, Complex Systems Studies, Kalamazoo College, USA
Luis Fuente, Computing and Communication Technologies, Oxford Brookes University, UK
Jean-Louis Giavitto, Music and Acoustics, IRCAM, France
David Halliday, Electronics, University of York, UK
Pauline Haddow, Computer and Information Science, NTNU, Norway
Okamoto Hiroshi, RIKEN Brain Science Institute, Japan
Arun Holden, Biomedical Sciences, University of Leeds, UK
Sam Marguerat, Clinical Sciences MRC, UK
Maizura Mokhtar, Automatic Control and Systems Engineering, University of Sheffield, UK
J. Manuel Moreno, Electronic Engineering, Technical University of Catalunya, Spain
Chrystopher Nehaniv, Computer Science, University of Hertfordshire, UK
Simon O'Keefe, Computer Science, University of York, UK
Cristina Costa Santini, Systems Biology, Technical University of Denmark
Tjeerd Olde Scheper, Computing and Communication Technologies, Oxford Brookes University, UK
Leslie Smith, Computing Science and Mathematics, University of Stirling, UK
Christof Teuscher, Electrical and Computer Engineering, Portland State University, USA
Alexander Turner, Electronics, University of York, UK
Jim Torresen, Informatics, University of Oslo, Norway
Juanma Vaquerizas, Max Plank Institute for Molecular Biomedicine, Munster, Germany

Invited speakers

Lee Altenberg

Kwang-Hyun Cho

Terry Gaasterland

Marco Salemi

Workshop

Anthony Newman
Senior Publisher, Elsevier

Organisers

Gary Fogel

Michael Lones

Stephen Smith

Andy Tyrrell

Submissions Due:

23rd March 2015
20th April 2015

Call for Papers:

Title image adapted from peasap (license).