Announcements


PeerJ collection for the HSCBB conference.

posted Aug 19, 2015, 4:25 AM by Georgios Pavlopoulos

Dear HSCBB Members,


We are pleased to announce that the proceedings of the HSCBB15 conference can be published as full-length papers in the newly affiliated PeerJ journal as a special PeerJ Collection for HSCBB15. Selected invitations will be sent to authors after the completion of the conference.


PeerJ is a respected open access publisher in the biological, medical and computer sciences. All published papers will become available online as open access. PeerJ is indexed by PubMed and Web of Science and has received a provisional 2,5-year impact factor of 2.1 and is expected to increase.

 

PeerJ has a unique business model for Open Access publication. Each author pays a single, low fee of $99 for the first time that he/she publishes in PeerJ journal. The same author is exempt from charges for a 5-year period even if he/she publishes with another combination of co-authors. Of course, co-authors who have not published in PeerJ journal before, will be asked to pay the one-time $99 fee.

PeerJ journal reviews submissions for scientific and methodological soundness and all articles submitted to PeerJ will go through a normal reviewing process. Abstract acceptance by the HSCBB15 conference does not guarantee that your manuscript will be accepted for full length publication.


Following discussions with PeerJ journal, we expect to maintain a long term collaboration in order to take full advantage of its 5-year publishing plan.


Instructions about the publishing costs and the plans can be found at: https://peerj.com/pricing/ and detailed guidelines for authors at: https://peerj.com/about/author-instructions/  


More details will be added in the HSCBB15 web page very soon.

MET-GR III workshop: Metabolic and Protein Network Analysis in Systems Biology

posted Jul 9, 2014, 1:38 AM by Georgios Pavlopoulos

Dear colleagues:

 

We are pleased to invite you to the MET-GR III workshop: Metabolic and Protein Network Analysis in Systems Biology, co-organized by the Institute of Chemical Engineering Sciences of the Foundation for Research and Technology – Hellas (FORTH/ICE-HT) and the University of Patras Research Network “Research and Applications in Medical Molecular Genetics - MGN”. MET-GR III constitutes the first summer school of the FP7 European Project in Synthetic Biology STREPSYNTH, sponsored also from the FORTH Systems Biology Network. It will take place at the Conference and Cultural Center of the University of Patras, September 18-20, 2014.

MET-GR III is the third in an international metabolomics workshop series in Greece started in 2008. This year, the workshop topics refer to the high-throughput metabolic and protein network activity analysis individually and/or in combination and include:

  • analytical methodologies
  • computational methodologies & network reconstruction
  • databases, ontologies, data analysis software

·         applications of these methodologies within systems/synthetic biology and medicine

MET-GR III includes presentations from several renowned scientists. Participation from graduate students and junior post-docs is strongly encouraged. I would greatly appreciate if you distribute this information to your groups, collaborators and other potentially interested colleagues.

Abstract Submission & Early Registration Deadline:  August 22, 2014

MET-GR III website : metgr3.iceht.forth.gr and contact e-mail: metgr3@iceht.forth.gr.

On behalf of the organizing committee

---------------------------------------------------------------------

Maria I. Klapa, Ph.D.

Principal Researcher (Rank B)

Head, Metabolic Engineering and Systems Biology Laboratory

Institute of Chemical Engineering Sciences (ICE-HT)

Foundation for Research and Technology, Hellas (FORTH)

Stadiou St., Platani,

P.O. BOX 1414, GR-26504

Patras, GREECE

Phone: +30-2610-965249

Fax: +30-2610-965-223

web: http://www.iceht.forth.gr/staff/klapa.html

Workshop: "Statistical Methods for Omics Data Integration and Analysis"

posted Jun 10, 2014, 1:29 AM by Georgios Pavlopoulos

Workshop: "Statistical Methods for Omics Data  Integration and 
Analysis"

Heraklion, Crete, Greece, November 10-12, 2014
 
Host and Venue: Foundation for Research and Technology, Hellas
http://smodia2014.com/
 
Important Dates:
20/08/2014                 Abstract Submission Deadline
10/09/2014                 Abstract Notifications
15/09/2014                 Early Registration Deadline
10/11/2014 – 12/11/2014    Workshop Dates
 
 
Objectives:
 
This workshop aims to bring together researchers in the fields of 
biology, bioinformatics, computational biology, statistics, 
biostatistics, machine learning, data mining, and pattern recognition 
that work on the analysis of omics data (e.g., transcriptomics, 
metabolomics, genomics) and particularly researchers that focus on 
developing new methods of integrating data, integrating their 
visualization, and integrating analysis of multiple and heterogeneous 
datasets. More details of the objectives of the workshop are here .
 
Programme:
 
The Workshop Programme consists of invited talks by prominent 
researchers in the field, presentations of extended abstracts, poster 
presentations, and social events.
 
Keynote Speakers:
 
A panel of prominent keynote speakers will present in the workshop:
 
    - John Storey , Princeton University
    - Michael Stumpf, Imperial College
    - Andrew Teschendorff, UCL, London
    - Sven Nelander, Uppsala University
 

In addition, the workshop will be attended by most STATegra partners.

Organized by: the STATegra consortium
 
STATegra (
stategra.eu) is an FP7 European project. The STATegra project 
aims to develop new statistical methods and tools for the integrative 
analysis of diverse omics data for a more efficient use of the genomics 
technologies. Furthermore we aim to make them readily available to the 
research community through rapid and efficient implementation as 
user-friendly software packages. Among the data-types we consider: 
mRNA-seq, miRNA-seq, Methyl-seq, Chip-seq, DNase-seq, Proteomics and 
Metabolomics. In addition we will develop methods for data gathering, 
management and integration in Knowledge Databases and Ontologies. We 
will deliver statistical methodologies to generalize meta-analysis of 
heterogeneous datasets (e.g., different experimental conditions) to 
address the issues of values missing-by-design, limited availability, 
poor quality (“dirty”) data and individually insufficiently powered 
studies.
 

STATegra partners supporting the Workshop are:
 
     -CLC bio (Denmark)
     -Biomax Informatics AG (Germany)
     -Karolinska Institutet (Sweden)
     -Imperial College of Science, Technology and Medicine (UK)
     -Foundation for Research and Technology – Hellas (Greece)
     -Institut d’Investigació Biomèdica de Bellvitge (Spain)
     -University of Amsterdam (Holland)
     -University of Leiden (Holland)
     -
Τhe Ludwig-Maximilians University of Munich (Germany)
     -University of California (USA)
     -Genomic of the Gene Expression Lab, Principe Felipe Research 
Centre (CIPF) (Spain)
 

 
Organizing  & Scientific Program Committee:
 
      -Ana Conesa, CIPF
      -David Gómez-Cabrero, Karolinska Institutet
      -Dieter Maier, Biomax
      -Veronica von Saint Paul, Biomax
      -Amanda Fisher, Imperial College London
      -Jesper Tegnér , Karolinska Institute
      -Ioannis Tsamardinos , FORTH
      -Johan Westerhuis, University of Amsterdam
      -Matthias Merkenschlager, Imperial College London
      -Roald Forsberg, CLC bio
      -Michael Lappe, CLC bio
      -Vincenzo Lagani,  FORTH
 
 
Submission:
 
We solicit papers with particular focus to the following areas:
 
       -Methods for retrieving related omics data, integrate them, and 
integratively visualize them
       -Methods for integrative knowledge discovery from multiple omics 
sources and biological knowledge
       -Methods for integratively analyzing multiple omics datasets and 
biological knowledge. The datasets may be obtained on the same or 
matched biological samples but employing different omics technologies 
and datasets obtained on different biological samples
       -Causal discovery methods for multiple omics datasets
       -Methods for integration and integrative analysis of time-course 
omics data
       -Methods for integrative network analysis stemming from multiple 
omics data and biological knowledge-bases
       -Innovative applications of statistical, machine learning, and 
data mining methods to multiple omics datasets and knowledge bases
       -Methods for interpretation and explanation of results obtained 
from various omics datasets and knowledge bases
 

The submissions should be 2-page abstracts. The Program Committee of 
the workshop will select a set of abstract to invite for expansion and 
inclusion in an Edited Volume in a high-impact journal (under 
negotiation). For abstract formats and submission instructions see the 
workshop site 
smodia2014.com

All aspects of the submission process will be handled online via the 
EasyChair Conference System at:

https://www.easychair.org/account/signin.cgi?key=11260915.R5ih2MfiVMi1Uw2r

Announcement of the NETTAB 2013 Workshop

posted Sep 29, 2013, 1:12 PM by Pantelis Bagos

Announcement of the NETTAB 2013 Workshop

Under the patronage of Bioinformatics Italian Society  and EMBnet

Scientific Programme of the NETTAB 2013 Workshop is available on-line at: http://www.nettab.org/2013/progr.php

A PDF copy is also available for downloading from:
http://www.nettab.org/2013/docs/ScientificProgramme.pdf

HSCBB13

posted Sep 25, 2013, 12:35 PM by Pantelis Bagos

Αγαπητοί συνάδελφοι και φίλοι,

Λόγω της καθυστερημένης ανάθεσης του φετινού συνεδρίου στη Λαμία, αλλά και ενός τεχνικού προβλήματος που αντιμετωπίζουμε στο Google Sites, το site του φετινού συνεδρίου δεν είναι ακόμη έτοιμο για να μπορέσετε να ενημερωθείτε. Επειδή τελικά το πρόβλημα δε λύνεται με τη Google (η οποία είναι ο host μας), μάλλον τελικά θα χρησιμοποιήσουμε την εναλλακτική διεύθυνση https://sites.google.com/site/hscbb13/home η οποία ακόμα δεν είναι έτοιμη. Σε λίγες μέρες το site θα είναι έτοιμο και θα ανακοινωθεί από εδώ. Μέχρι τότε να σας ενημερώσω ότι:

Α) Η ημερομηνία διεξαγωγής του συνεδρίου είναι 22-24 Νοεμβρίου.  Για να μπορέσουμε να προγραμματίσουμε καλύτερα τον αριθμό των παρευρισκόμενων, θα μπορούσατε όσοι θέλετε σίγουρα να παρευρεθείτε, να συμπληρώσετε τη λίστα στο παρακάτω Doodle Poll:

http://doodle.com/dzfr3it934a92uh4


Β) Η καταληκτική ημερομηνία για την κατάθεση των εργασιών θα είναι η 3 Νοεμβρίου του 2013. Η κατάθεση θα γίνει μέσω του EasyChair στην παρακάτω διεύθυνση:

https://www.easychair.org/conferences/?conf=hscbb13


Γ) Το κόστος συμμετοχής θα είναι φέτος μικρότερο από τις άλλες φορές, όπως φαίνεται στον πίνακα που επισυνάπτω από το υπο κατασκευή site. Το early registration θα γίνει μέσω κατάθεσης στον τραπεζικό λογαριασμό της ΕΕΥΒΒ.

Ζητώ συγνώμη για την καθυστέρηση. Η κατανόηση σας είναι πολύτιμη.
Ελπίζω να σας δω από κοντά στη Λαμία.

Παντελής Μπάγκος
Εκ μέρους της ΕΕΥΒΒ και της Οργανωτικής Επιτροπής






Early registration fee
(up to 7-11-13)
Late registration fee
(up to 22-11-13)
Non HSCBB members HSCBB members* Non HSCBB members HSCBB members*
  • Student: 35 €
  • Senior:   60 €
  • Industry: 100 €
  • Student: 20 €
  • Senior:  30 €
  • Industry: 80 €
  • Student: 45 €
  • Senior:   80 €
  • Industry: 120 €
  • Student: 30 €
  • Senior:   50€
  • Industry: 100 €

As students, are considered the people at their undergraduate, postgraduate and pre-doctoral level of studies.

* For HSCBB members, the society's annual membership fee will be paid on site. This amounts to 5€ for students and 20€ for senior scientists.

Registration fees include:  

  • Reception
  • Coffee and Lunch breaks
  • Conference Program and Electronic Proceedings Volume

Tickets for the conference's dinner can be purchased online and onsite. The cost is 15€  for participants and 25 €  for accompanying persons. 
 

Meeting Report: The Seventh Conference of the HSCBB

posted Jun 25, 2013, 4:05 AM by Pantelis Bagos   [ updated Jun 25, 2013, 4:05 AM ]

http://journals.sfu.ca/rncsb/index.php/csbj/article/view/csbj.201303006/263


Meeting Report: The Seventh Conference of the Hellenic Society for Computational Biology and Bioinformatics

 

 

Stavros J Hamodrakas a, Ioannis Iliopoulos b, Christos A Ouzounis c,d,*, Pantelis G Bagos e, Vasilis J Promponas f

 

 

The Hellenic Society For Computational Biology and Bioinformatics (HSCBB) was conceived as a trans-national society, representing two countries that share the same language and history, Cyprus and Greece. The first, unofficial meeting was held in Heraklion in 2006, followed by Athens in 2007 and Thessalonica in 2008. After the formation of the Society and its ‘inaugural’, fourth scientific conference in Athens during 2009, the HSCBB organized two meetings in Alexandroupolis and Patras, with the aspiration to provide the necessary exposure of graduate students to new developments, expand its horizons towards the international community, promote the development of the field and formulate a solid agenda for the future, all consistent with its primary goals (http://www.hscbb.gr). The HSCBB12 meeting, which took place in Heraklion confirmed that, even in a period of austerity and societal crisis, the local community is increasingly active.

 

Thanks to the support of national and international sponsors, including the Computational and Structural Biotechnology Journal, the HSCBB12 has been an unprecedented success. Approximately 100 participants have registered, providing for the first time a much clearer picture of activities of the bioinformatics communities in the two countries and material for a mapping exercise undertaken by the HSCBB, as a vehicle for further growth. One verdict from this analysis has been that today, unlike seven years ago, all major academic centers in the two countries have acquired some bioinformatics activity, with a wide range of expertise, much depending on the local needs of the corresponding organizations.

 

Four keynote speakers provided a wider perspective of translational bioinformatics in their own special fields: Manolis Dermitzakis (University of Geneva) on human population genomics, Anton Enright (European Bioinformatics Institute) on miRNA computational genomics, Alice McHardy (Max‐Planck‐Institut für Informatik) on human influenza A virus evolution, and Alexis Stamatakis (Heidelberg Institute for Theoretical studies) on computational challenges in biodiversity informatics. Moreover, another four invited speakers covered diverse, yet more practical areas in the field: Graham Ball (Nottingham Trent University) on pathway modelling, Guy Cochrane (European Bioinformatics Institute) on the European Nucleotide Archive, Ioannis Kontodinas (Biomax Informatics) on knowledge management for systems biology, and Kitsos Louis (IMBB-FORTH) on the role of ontologies in modern biology. All these contributions were highly appreciated by their audiences.

 

The topics covered by the conference included the following areas:

  • structural bioinformatics (interaction site analysis, sequence-based structural classification, molecular recognition feature analysis);
  • sequence analysis (transcriptome analysis, SNP analysis, structural variomics);
  • systems biology (stochastic modeling of protein dynamics, metabolomics, epigenomics);
  • gene regulation and miRNA (miRNA profiling, miRNA duplex prediction, miRNA ontologies);
  • algorithms, methods & tools (tree pruning algorithms, GPU accelerators, scientific workflow management systems);
  • applied/translational bioinformatics (cell signaling simulations, text mining, evolutionary bioinformatics, data integration, biomarker discovery);
  • genome and comparative biology (gene duplication detection, microbial genome annotation, pangenome analysis).

 

The list of the 70 or so contributions (20 oral presentations, 38 posters, 4 invited presentations, 1 three-day workshop, plus the 8 keynote and invited lectures) has exceeded expectations for another reason. For the first time, contributions at the HSCBB conference had a significant number of co-authorships with multiple, highly prestigious institutions, including the EBI, the Joint Genome Institute at Berkeley, and Imperial College London.

 

In total, according to one study published a few years ago in the HSCBB10 proceedings, 400 papers from 63 institutions have been published in one generation, with an exponential increase during the past decade, indicating that bioinformatics have now taken root in Greece and Cyprus, with a new generation of scientists acquiring the expertise and the ability to instigate new research and education programs. According to another bibliometric study, also published in the HSCBB10 proceedings, there is still scope for growth both in quantity and quality. Greece can potentially increase the number of bioinformatics laboratories from a dozen or so today to over 30 while Cyprus might also develop bioinformatics from a handful of teams to twice that number. Moreover, the impact of HSCBB in the literature is comparable to that of Australia and New Zealand, if the GDP per capita rank of the two pairs of countries is taken into account. In other words, Greece and Cyprus have reached a level where their computational biology communities arguably have a respectable standing on the world stage. As pointed out elsewhere, the field has now grown to a point that biological research is virtually impossible without computation, so that even smaller countries do have a role in this collective effort worldwide (http://www.ploscollections.org/article/browseIssue.action?issue=info%3Adoi%2F10.1371%2Fissue.pcol.v03.i03).

 

We hope that the effort of the HSCBB members will ultimately generate the interest of the international community and establish a presence beyond the borders of Greece and Cyprus.

 

 

aFaculty of Biology, Department of Cell Biology and Biophysics, University of Athens, Athens, Greece

bDivision of Medical Sciences, University of Crete Medical School, Heraklion, Greece

cInstitute of Applied Biosciences, Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece

dDonnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario, Canada

eDepartment of Computer Science and Biomedical Informatics, University of Central Greece, Greece

fBioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus.

 

* Corresponding author.

E-mail address: christos.ouzounis@me.com (Christos A Ouzounis)

Greece latest country to sign ELIXIR MoU

posted Jun 18, 2013, 3:30 AM by Pantelis Bagos

Wed 30-01-2013

ELIXIR MoU now has signature of 15 countries and EMBL

Hinxton, 30 January 2013 – Greece is the latest country to join ELIXIR, the pan-European undertaking to safeguard the results of life science research. The ELIXIR Memorandum of Understanding (MoU) is a first formal but non-binding step towards the implementation of ELIXIR. Greece is the 15th nation to demonstrate its commitment to ELIXIR through signature of the MoU.  

The purpose of ELIXIR is to construct and operate a sustainable infrastructure for biological information in Europe to support life science research and its translation to medicine and the environment, the bio-industries and society. ELIXIR will harness the strength of Europe’s current bioinformatics providers, ensuring that biological data and services being run by participating organisations are integrated in a way of most value to life science researchers. The first five pilot projects to begin this integration are already underway.    

“Joining ELIXIR is an important step for Greece. We know the value of being part of European research infrastructures – particularly when they help us maximise the benefits of investments we’ve already made. Joining ELIXIR is part of Greece’s strategy to boost R&D both in the business and academic sector,” explains Professor Babis Savakis, President and Scientific Director of the Alexander Fleming Biomedical Sciences Research Centre and Greek Scientific Delegate to the ELIXIR Interim Board.

“Greece’s commitment to ELIXIR will result in tangible long-term scientific and economic benefits and its decision to join at this time, in the face of serious economic challenges, is truly impressive,” said Professor Søren Brunak of the Technical University of Denmark, Chair of the ELIXIR Interim Board. “This is an exciting time as ELIXIR now enters its implementation phase and the first technical pilot projects are underway. I look forward to Greece playing a full role in contributing to the successful operation of ELIXIR.”

Greece joins the European Molecular Biology Laboratory (EMBL) and 14 signatory nations; the Czech Republic, Denmark, Estonia, Finland, Israel, Italy, the Netherlands, Norway, Portugal, Slovenia, Spain, Sweden, Switzerland and the United Kingdom. Further countries are expected to join ELIXIR over the coming months.


http://www.elixir-europe.org/news/greece-latest-country-sign-elixir-mou

Call for abstracts - HSCBB12

posted May 10, 2012, 2:48 AM by Pantelis Bagos   [ updated May 10, 2012, 2:48 AM ]

Call for abstracts

7th conference of the
Hellenic Society for Computational Biology and Bioinformatics - HSCBB12


Date:  October 4-6, 2012
Venue: Foundation for Research and Technology - Hellas (FORTH)
City:  Heraklion, Greece
URL:   http://hscbb12.hscbb.gr/

(in conjunction with the Workshop on Biodiversity, October 1-3 at the
Hellenic Center for Marine Research http://innovator.ath.hcmr.gr/newhcmr1/)

Abstract Submission Dates:    May 15 - July 15, 2012
Early Registration:            July 1 -  Aug 30, 2012

Aim & Scope

The annual HSCBB conference aims to provide an interdisciplinary forum to researchers in Computational Biology, Bioinformatics, as well as practitioners applying computational methods in their biological or biomedical research. The conference aims to bring together researchers in the region to discuss on-going research projects and exchange ideas.

Abstract Submission

Authors are invited to submit 2-page abstracts describing on-going work that includes at least some new results not published elsewhere. Submissions are electronic from the HSCBB 2012 website following the format of the provided template. The abstracts should be written in English.

Conference Program

The conference program includes highly-regarded invited speakers in the field and a special industrial session where representatives from bioinformatics companies will present products and research results of their companies. A selected number of representative accepted abstracts will be orally presented, while the rest of the accepted abstracts will be presented as posters. The program includes a dinner Banquet in a tradition Cretan tavern. The conference language is English.

Future details and important announcements will be available at the conference web-site.

Organizing Institutions

The Hellenic Society for Computational Biology and Bioinformatics
Institute of Molecular Biology and Biotechnology - FORTH
Institute of Computer Science - FORTH
Hellenic Center for Marine Research - HCMR
University of Crete

The HSCBB Board / Organizing Committee

Hamodrakas Stavros    University of Athens, Greece
Iliopoulos Ioannis    University of Crete, Greece
Ouzounis Christos        King’s College, London, U.K.
Promponas Vasilis        University of Cyprus, Nicosia, Cyprus
Bagos Pantelis        University of Central Greece

Local Organizers

Poirazi Panayiota (Chair)    IMBB - FORTH
Kotoulas George    IMBG-HCMR
Oulas Anastasios    IMBG-HCMR
Potamias George    ICS-FORTH
Tsamardinos Ioannis    ICS-FORTH / University of Crete
Iliopoulos Ioannis    University of Crete, Greece
Nikolaou Christoforos    University of Crete, Greece

Announcing HSCBB12

posted Mar 20, 2012, 12:47 PM by Pantelis Bagos

The 7th Conference of the Hellenic Society for Computational Biology & Bioinformatics – HSCBB12 – is co-organized by the Hellenic Society for Computational Biology and Bioinformatics (HSCBB) jointly with the Institutes of Computer Science and Molecular Biology and Biotechnology of the Foundation for Research and Technology-Hellas (FORTH) and the  Hellenic Center for Marine Research (HCMR).  HSCBB12 will take place at FORTH in October 4 - 6, 2012.

As an outreach activity of the HSCBB, a satellite Workshop on Biodiversity with training lectures and panel discussions will also be organized (October 7-9, 2012) at HCMR.

The Conference, which is the major annual event of HSCBB, aims at being a forum for researchers in the relevant fields from Greece, Cyprus and other countries to present their work and creatively interact for the establishment of scientific networks and collaborations.


HSCBB11 photos

posted Oct 17, 2011, 12:23 AM by Hellenic Society for Computational Biology and Bioinformatics

Photos from the conference are available here:
http://hscbb11.hscbb.gr/home/photos

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