SSBSS 2016

International Synthetic and Systems Biology Summer School


Biology meets Computer Science and Engineering


8 - 14 July 2016, Volterra (Pisa) Tuscany, Italy

Summary

SSBSS 2016 DEADLINES:

  • Early Application: May 26, 2016
  • Notification Acceptance: from April 2 to May 28, 2016

  • Late Application: from May 27 to July 4th 2016
  • Notification Acceptance: from May 29 2016 according to registration time

  • Early Short Talk/Poster Submission: May 26, 2016
  • Notification Acceptance: from April 2 to May 28, 2016

  • Late Short Talk/Poster Submission: from May 27, to July 4th 2016
  • Notification of Decision for Oral/Poster Presentation: from May 29, 2016 according to submission time

  • Early Registration: by June 30, 2016
  • Late Registration: After June 30, 2016
  • Recent advances in DNA synthesis have increased our ability to build biological systems. Synthetic Biology aims at streamlining the design and synthesis of robust and predictable biological systems using engineering design principles. Designing biological systems requires a deep understanding of how genes and proteins are organized and interact in living cells: Systems Biology aims at elucidating the cellular organization at gene, protein and network level using computational and biochemical methods.

    The Synthetic and Systems Biology Summer School (SSBSS) is a full-immersion five-day residential summer school at the Volterra Learning Center (Pisa - Tuscany, Italy) on cutting-edge advances in systems and synthetic biology with lectures delivered by world-renowned experts. The school provides a stimulating environment for students (from Master students to PhD students), Post-Docs, early career researches, academics and industry leaders. Participants will also have the chance to present their results, and to interact with their peers, in a friendly and constructive environment.

    Speakers

    • Yaakov (Kobi) Benenson, Synthetic Biology Group@Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
    • Leonidas Bleris, Bioengineering Department, The University of Texas at Dallas, USA
    • Edoardo Boncinelli, Universita' Vita-Salute San Raffaele, Milano, Italy
    • John Cumbers, Founder SynBioBeta, Mountain View, CA, USA
    • Domitilla Del Vecchio, Department of Mechanical Engineering, MIT, USA
    • Diego Di Bernardo, Dept of Chemical Materials and Industrial Production Engineering University of Naples "Federico II", Naples, Italy
    • Barbara Di Ventura, Synthetic Biology Group - BioQuant/DKFZ, Heidelberg, Germany
    • J. Gootenberg, Feng Zhang and Aviv Regev Groups, Department of Systems Biology, Harvard Medical School, Harvard University, USA
    • Markus Herrgard, Technical University of Denmark - Biosustain, Novo Nordisk Foundation Center for Biosustainability, Denmark
    • Shalev Itzkovitz, Department of Molecular Cell Biology, Weizmann Institute of Science, Israel
    • Francesco Ricci, Dipartimento di Scienze e Tecnologie Chimiche, University of Rome Tor Vergata, Rome, Italy

    Topics

    • Genetic Engineering
    • Metabolic Engineering
    • Reading and Writing Genomes
    • Synthetic Genomes
    • Synthetic Circuits and Cells
    • Artificial Tissues and Organs
    • Genomically Recoded Organisms
    • Genome Design
    • Pathway Design
    • Biological Design Automation and Biological CAD
    • Genome Engineering
    • Cellular Systems Biology
    • Experimental Synthetic Biology
    • Computational Synthetic Biology
    • Stochastic Gene Regulation
    • Gene Signaling
    • Quantitative Molecular Biology
    • High-throughput Techniques
    • Biological Engineering
    • Industrial Synthetic and Systems Biology

    News:

    Tuscany - Volterra

    Speakers and Lectures

    • Yaakov (Kobi) Benenson, Synthetic Biology Group@Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
    • Lecture 1: "The Practice of Mammalian Synthetic Biology"
      Lecture 2: "Mammalian Cell Classifiers"

    • Leonidas Bleris, Bioengineering Department, The University of Texas at Dallas, USA
    • Lecture 1: "Genome Editing Technologies and Therapeutic Modalities"
      Lecture 2: "Benchmark Circuits and Topological Properties"

    • Edoardo Boncinelli, Universita' Vita-Salute San Raffaele, Milano, Italy
    • Lecture : "TBA"

    • Domitilla Del Vecchio, Department of Mechanical Engineering, MIT, USA
    • Lecture 1: "Modularity in genetic circuits: Dream versus Reality"
      Lecture 2: "Engineering Modularity in Genetic Circuits"

    • Diego Di Bernardo, Dept of Chemical Materials and Industrial Production Engineering University of Naples "Federico II", Naples, Italy
    • Lecture 1: "Engineering and Control of Biological Circuits in Yeast"
      Lecture 2: "Engineering and Control of Biological Circuits in Mammalian Cells"

    • Barbara Di Ventura, Synthetic Biology Group - BioQuant/DKFZ, Heidelberg, Germany
    • Lecture 1: "Using Blue Light to Control Protein Localization in Living Mammalian Cells"
      Lecture 2: "Using Split Inteins for Protein Engineering in Living Cells"

    • J. Gootenberg, Feng Zhang and Aviv Regev Groups, Department of Systems Biology, Harvard Medical School, Harvard University, USA
    • Lecture 1: "Discovering and Characterizing CRISPR effectors"
      Lecture 2: "Probing Biology with CRISPR Screening"

    • Markus Herrgard, Technical University of Denmark - Biosustain, Novo Nordisk Foundation Center for Biosustainability, Denmark
    • Lecture 1: "Developing an Integrated Cell Factory Design Tool"
      Lecture 2: "Using Automated Laboratory Evolution to Optimize Cell Factories"

    • Shalev Itzkovitz, Department of Molecular Cell Biology, Weizmann Institute of Science, Israel
    • Lecture 1: "Single Molecule Approaches for Studying Gene Expression in Intact Mammalian Tissues"
      Lecture 2: "Systems Biology of Stem Cell-Maintained Tissues"

    • Francesco Ricci, Dipartimento di Scienze e Tecnologie Chimiche, University of Rome Tor Vergata, Rome, Italy
    • Lecture 1: "DNA Nanotechnology Tools and Reactions for Synthetic Biology"
      Lecture 2: "Nature-inspired DNA-based Nanodevices"

    • More speakers will be announced soon!

    Industrial Panel

    • John Cumbers, Founder SynBioBeta, Mountain View, CA, USA
    • Lecture: "TBA"

    Next Generation Sequencing Workshop

    July 12th, 2016

    • Lecture: "How Fast can we Align Sequences?", Mario Guarracino, CNR, Italy

      Sequence alignment consists in the comparison of two or more strings to find similarities between the sequences. Each symbol of a string is assigned to at most one (maybe none) symbol in another string. These similarities are particularly important when the sequences represent biological molecules, such as DNA, RNA and proteins, because we assume that similar sequences hold a similar function, structure, and there might be an evolutionary relationships. In this lecture, we will address the issue of sequence similarity. We will introduce the concept of sequence alignment, and the concept of sequence similarity in terms of distance between symbols. Given a matrix of similarities between all possible pairs of symbols, the similarity of the alignment is the sum of the similarities between the aligned symbols. The problem is to find the alignment between two sequences having the maximum similarity (minimum distance). A global search in the space of all possible alignments is computationally impractical, and we will see how dynamic programming efficiently solves the problem. We will devote some time to the problem of finding local and local alignments between sequences. Finally we will focus on algorithms where short sequences need to be compared to a reference. This is often the case with next generation sequencing technologies, in which ten of millions of short strings need to be locally matched on a long one. A wide variety of alignment algorithms have been developed over the past few years and we will discuss their properties and applications on different types of experimental data.

    • Lecture: "Advanced Bioinformatics Tools for NGS" - TBC, Luca Zammataro, Yale University, USA - TBC

      TBA

    • Tutorial: "Detection and Analysis of Contaminating Sequences in NGS Sequencing Data", Ilaria Granata, CNR, Italy

      Time duration: 2 hours (45 minutes Presentation + 1hour 15minutes Practical tutorial)

      Reads alignment is an essential step of NGS data analyses. One challenging issue is represented by unmapped reads that are usually discarded and considered as not informative. However, it is important to fully understand the source of those reads, to assess the quality of the whole experiment. Moreover, is of interest to get some insights on possible contamination from organisms other than the one under investigation that might be present in the sequenced samples. Contamination may take place during the experimental procedures leading to sequencing, or be due to the presence of microorganisms infecting the sampled tissues. We will present a new pipeline aimed to the detection of viral, bacterial and fungi contamination in human sequenced data. The contaminating sequences can be filtered out from total reads in fastq or fasta formats and detected after the alignment to better understand their origin and correlation to the object of study. To this extend, data are sorted by organism and classified by taxonomic group.
      Description:
      1) Theoretical explanation of the topic and the state of art (Presentation);
      2) Illustration of the new pipeline and workflow (Practical);
      3) Application of the pipeline to a case study and discussion of the results (Practical).


    • Tutorial: "Detection and Interpretation of Circular RNAs in RNA-seq Experiments", Parijat Tripathi, CNR, Italy

      Time duration: 2 hours (45 minutes presentation + 1 hour 15minutes: Practical tutorial)

      Circular RNAs are a large class of animal RNAs with regulatory potency. In the few unambiguously validated circRNAs in animals, the spliceosome seems to link the 5' and downstream 3' ends of exons within the same transcript. There are number of tools available to detect circular RNA such as CIRI, segemehl, find_circ and CIRCexplorer. In this tutorial, we focus on CIRCexplorer tool to identify circular RNA. Basically CIRCexplorer based on combined strategy to identify junction reads from back splices exons and introns lariats. At present it is only a circular RNA annotating tool, and it parses fusion junction information from mapping results of other aligners. In the tutorial, we try to identify these junction reads from unmapped reads after alignment is carried out for normal reads. CIRCexplorer need number of prerequisite steps which should be further carried out before running this tools. We have developed a computational pipeline using CIRCexplorer and all the other dependencies to identify Circular RNA in a given sample of RNA-seq data. We also added some more in house-built script to compare two different samples, for example disease vs. normal condition with respect to the expression of circular RNA and also try to understand the functional importance of Circular RNA harboring regions.

      Description:
      1) Introduction to mapping strategy to obtain junction reads for circular RNAs;
      2) Running in house built wrapper pipeline using CIRCexplorer to obtain the results;
      3) Parsing the results for functional annotation and comparative studies between different samples.


    School Directors

    Scientific Committee

    • Giuseppe Nicosia, University of Catania, Italy
    • Jole Costanza, Italian Institute of Technology, Italy
    • Barbara Di Camillo, University of Padova, Italy
    • Simone Furini, University of Siena, Italy
    • Emanuele Domenico Giordano, University of Bologna, Italy
    • Massimo Gulisano, University of Catania, Italy
    • Mario Guarracino, ICAR-CNR, Italy
    • Markus Herrgard, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
    • Paolo Magni, University of Pavia, Italy
    • Vincenzo Manca, University of Verona, Italy
    • Giancarlo Mauri, University of Milano Bicocca and SYSBIO - Center of Systems Biology, Italy
    • Giuseppe Narzisi, New York Genome Center, USA
    • Wieslaw Nowak, Nicholas Copernicus University, Poland
    • Danilo Porro, University of Milano Bicocca, Italy
    • Francesco Ricci, University of Rome "Tor Vergata", Italy
    • Gianna Maria Toffolo, University of Padova, Italy
    • Renato Umeton, MIT, USA
    • Luca Zammataro, Yale University, USA

    Deadlines

    • Early Application: May 26, 2016
    • Notification Acceptance: from April 2 to May 28, 2016

    • Late Application: from May 27, to July 4, 2016
    • Notification Acceptance: from May 29th 2016 according to registration time

    • Early Short Talk/Poster Submission: May 26, 2016
    • Notification Acceptance: from April 2 to May 28, 2016

    • Late Short Talk/Poster Submission: from May 27, to July 4, 2016
    • Notification of Decision for Oral/Poster Presentation: from May 29, 2016 according to submission time
    • Early Registration: by June 30, 2016
    • Late Registration: After June 30, 2016

    Florence - Old bridge

    Application Form

    The school will be open up to 100 150 qualified, motivated and selected students. Undergraduate and graduate students, post-docs, research fellows, academics and industrial professionals are encouraged to apply. School fees will be 550 EUR for undergraduate and graduate students, 650 EUR for post-docs and research fellows and 750 EUR for all other participants (the late registration fees are the following: 600 EUR for undergraduate and graduate students, 700 EUR for post-docs and research fellows and 800 EUR for all other participants ). Fees will cover lectures, course materials, coffee breaks, social tour in Florence, and Wi-Fi Internet Connection.

    The School will involve a total of 32 hours of lectures, the final achievement will be equivalent to 8 ECTS points (ECTS grading scale) for the PhD students attending the summer school; during the summer school the students will tackle homeworks/projects.

    Early Applications should be received before May 26, 2016. Applicants will receive notification of acceptance from April 2 to May 28, 2016 according to registration time.

    Cancellation policy: cancellations received no later than May 31, 2016 will receive a full refund less 50 Euro in processing charges. After May 31, 2016 no refunds will be given.

    Privacy Policy

    VISA

    You need a valid passport to enter Italy. It is highly recommended that passports have at least six months validity remaining after your intended date of departure from your travel destination. A visa is not required for citizens of EU, USA, Canada, Australia, Japan, and several other countries: please, check your visa requirements here. Visitors who need a visa should apply for a standard Schengen visa.

    Short Talk and Poster Submission

    Students may submit a research abstract (1 page) for presentation using the Application Form. School directors will review the abstracts and will recommend for poster or short-oral presentation. The poster should be written in English. For your poster, a board will be provided which measures A0 size (118.9 cm high and 84.1 cm wide, respectively 46.8 x 33.1 inch). You need to print and bring with you the poster to the school. Push tacks or velcro adhesive will be provided at the school venue to mount your poster to the board. Abstract should be submitted by May 26, 2016. The abstracts will be published on the electronic hands-out material and on the web site of the summer school.

    Tuscany - Pisa

    Sponsors

    Platinum Sponsors:

    • TBA



    Gold Sponsors:

    • TBA



    Silver Sponsors:

    • Leonardo Design Systems Inc.



    Bronze Sponsors:

    • TBA



    SSBSS welcomes Sponsors, for more information send an email to: ssbss.school@gmail.com

    Venue and Accommodation

    Location

    SSBSS will be hosted in SIAF Learning Village Volterra (Pisa) Tuscany, Italy (Google Map) at the venue "SIAF Learning Village - Volterra (Pisa)" that offers transfer to/from Pisa International Airport - Galileo Galilei (PSA).
    Plenary talks and introductions to the poster sessions will be held in one of the main conference rooms while the actual poster sessions will be held in the other main room.

    SIAF - The Learning Village in Tuscany
    SP del monte Volterrano
    Localita' Il Cipresso
    56048 Volterra (Pisa) Tuscany, Italy
    Phone.: (+39) 0588 81266 - 86855
    Fax.: (+39) 0588 86414
    email: info@siafvolterra.eu
    http://www.siafvolterra.it/wp/en/how-to-reach-us/
    GPS data:
    Latitude: N 43° 24' 3.99''
    Longitude: E 10° 50' 46.78''

    Volterra is 72 kilometers from Florence, 50Km from Siena, 30Km from San Gimignano and 63Km from Pisa, capital of the province to whom the municipality belongs. You can reach Volterra by car or bus, and if necessary, the SIAF can arrange shuttle services from the train stations of the major cities of Tuscany and from the airports of Pisa and Florence. Coming from North Italy you can reach Volterra via Pisa or Florence away. Coming from the south you can reach via Volterra Siena or via Cecina (LI).

    Travel to Volterra

    Plane
    Pisa "Galileo Galilei" International Airport (PSA) is the nearest and most convenient airport at some 63km from Volterra.

    Train
    TreniItalia.

    Volterra, Valdicecina
    Visit, Stay, Enjoy Volterra - Valdicecina, Tuscany

    Info

    The 7 UNESCO World Heritage Sites in Tuscany:

    Accommodation

    Accommodation and Transfer Reservation at SIAF Learning Village Tuscany - Volterra

    SSBSS 2016 participants will be hosted at the SIAF Learning Village Tuscany - Volterra (SSBSS 2016 workshop venue) at very special rates. Depending on availability, rooms (single, double, triple) will be assigned on a first-come, first-served basis!. SSBSS 2016 participants must make reservations for accommodation as soon as possible (no later than June 20, 2016) using accommodation reservation form to be sent by email to SIAF Learning Village - Tuscany: giada.ragoni@siafvolterra.eu Dr. Giada Ragoni. After June 20 2016 there is no guarantee for reservations in SIAF Learning Village - Tuscany.

    If SIAF Learning Village is fully booked Volterra offers a wide choice of Hotels, B&Bs, and Apartments. At the following links you can find some other kinds of accommodations:

    Tuscany - Hills

    Contacts

    TaoSciences Research Center
    Italy
    http://www.taosciences.it

    For more information, send an email to: ssbss.school@gmail.com

    SSBSS Facebook.