SEEK News

Thursday, December 17, 2015 - 15:24

We are pleased to announce the release of SEEK version 1.0.

This version of SEEK forms the base version for our new https://fairdomhub.org service, about which we will be releasing more details in the new year.

Included in this version are some key new features:

  • Support for the self creation and administration of Programmes, and Projects within them. If this feature is enabled, users will be able to setup their own Programmes and support them without the need of a full SEEK administrator other than their initial activation.
  • A refinement of the administrative roles.
  • Publishing of entire Investigations as Snapshots - frozen in time as Research Objects (see http://researchobject.org), along with a DOI. In the future we will be extending this to also support more fine-grained Studies and Assays.

There have been many other smaller improvements and changes, more details of which can be found at http://docs.seek4science.org/tech/releases/ .

We have also started setting up a new Documentation site available at http://docs.seek4science.org/ where we will be publishing technical developer information, and also more in depth user guides and information. This is now integrated with SEEK, and replaces the old internal help system.

With this version we are deprecating the old BioSamples - which we will be replacing with a much improved Sample system during the early part of 2016. Please visit our Roapmap at http://docs.seek4science.org/tech/roadmap.html . We will release more information about Samples early next year.

Details on how to install or upgrade to this version can be found at http://docs.seek4science.org/get-seek.html

After 7 years of continuous development, 1.0 marks a major milestone. Many thanks to those that have contributed and supported us in our ongoing journey.

 

- THE FAIRDOM Team

Wednesday, October 1, 2014 - 10:06

... FROM STRUCTURAL BIOINFORMATICS TO INTEGRATIVE SYSTEMS BIOLOGY

October 1st is the last day to register online for a reduced fee.

Below is a summary of the talks. More information and details on how to register can be found at http://www.nettab.org/2014/

KEYNOTE TALKS

Thursday October 16, 2014, 9:15 AM
Interactomics: Computational Analysis of Novel Drug Opportunities
Ram Samudrala, University of Washington, Seattle, USA

Thursday October 16, 2014, 2:20 PM
Biomodel engineering with Petri nets
Wolfgang Marwan, Otto-von-Guericke Universität, Magdeburg, Germany

Friday October 17, 2014, 9:00 AM
Modeling protein structures and complexes using evolutionary information
Torsten Schwede, SIB Swiss Institute of Bioinformatics & Biozentrum University of Basel, Switzerland

Friday October 17, 2014, 2:00 PM
Crystallizing macromolecular complexes: the ribosome
Ada Yonath, Weizmann Institute of Science, Rehovot, Israel

SPECIAL GUEST TALKS

Thursday October 16, 2014, 12:00 PM
Understanding protein–protein contacts on a PDB-wide scale
Guido Capitani, Paul Scherrer Institute, Villigen, Switzerland

Thursday October 16, 2014, 1:30 PM
From genes to networks and to dynamic models
Lilia Alberghina, SYSBIO Centre of Systems Biology, University of Milano-Bicocca, Italy

TUTORIALS

Wednesday October 15, 2014, 14:30 – 16:15
Modelling Interactomes: From Genotype to Phenotype
Ram Samudrala, University of Washington, Seattle, USA

Wednesday October 15, 2014, 16:45 – 18:30
Protein Engineering and Drug Design Based on 3D Protein Models
Gianfranco Gilardi, University of Torino, Italy

Wednesday October 15, 2014, 14:30 – 18:30 (30' break included)
Next generation data analysis using OneChannelGUI
Raffaele Calogero, University of Torino, Italy
and Francesca Cordero, University of Torino, Italy

ORAL COMMUNICATIONS

GELA: Gene Expression Logic Analyzer
Emanuel Weitschek, Giulia Fiscon, Giovanni Felici and Paola Bertolazzi

The mirror images in protein structure reconstruction and their energy terms
Monika Kurczynska, Bogumil Konopka and Malgorzata Kotulska

Analysis of capture-based bisulfite sequencing data with ERNE-BS5
Nicola Prezza, Francesco Vezzi, Max Kaller and Alberto Policriti

A combination of transcriptional and microRNA regulation improves the stability of the relative concentrations of target genes
Andrea Riba

The miRNA Action Mechanism Defines Dynamics and Noise Buffering in Feed Forward Loops
Alexander Samsonov, Maria Duk and Maria Samsonova

Sequence based model of gap gene regulatory network
Maria Samsonova, Konstantin Kozlov, Vitaly Gursky and Ivan Kulakovsky

Effect of mutations to HIV-1 PR . Insights into Drug Resistance and Drug Design: A Molecular Dynamics Approach
Haralambos Tzoupis

First passage time problems in gene expression
Alma Dal Co

From the inference of molecular structures to the analysis of emergent cellular dynamics: Accelerating the computational study of biological systems with GPUs
Daniela Besozzi, Marco S. Nobile, Paolo Cazzaniga, Davide Cipolla and Giancarlo Mauri

Role of Transposable Elements in fine-tuning alternative splicing
Alessandro Testori and Michele Caselle

Discovering the Escherichia coli nutritional phase space from a compendium of environmental conditions
Claudio Angione and Pietro Liò

From genome to molecular networks, a plug-in to map next generation sequencing data to protein interactions and their structures with the Integrated Genome Browser
Arnaud Ceol and Heiko Muller

Integrative strategies for omics data: ERalpha cistrome and epigenome case-study
Giulio Ferrero, Valentina Miano, Gianfranco Balbo, Michele De Bortoli, Marco Beccuti and Francesca Cordero

Topological SHAPE analysis of RNA structure by persistent homology
Adane Mamuye, Emanuela Merelli and Matteo Rucco

Trends in structural coverage of the protein universe
Kamil Khafizov, Carlos Madrid-Aliste, Almo Steven and Andras Fiser

Thursday, July 24, 2014 - 11:17

6th – 7th October, Studio Villa Bosch, Heidelberg, Germany.

Dear Colleagues,

Addressing data management needs in systems biology is both a vital and challenging task that we as a community need to address. Following the success of the Systems Biology Software Developers Workshop in 2012, we are proposing a second in the series to bring together like-minded scientists that are working on these challenges, so we can update, and forge plans and collaborations for the future.

Participation is limited to 25 people, and intended participants are software developers working in the field of data management in biology.

    If you want to participate you should be:
  • Fluent in at least one programming language
  • Daily working as either a programmer or as someone concerned with software engineering or code audit.
  • Willing to participate in discussions about the (technical) future and extensibility of the software project you are involved with.

Participation in the workshop is free. However, participants have to bear travel and accommodation costs by themselves, and we reserve the right to pick participants.

More information can be found at on our website: http://fair-dom.org/wiki/foundry_workshop.

Wednesday, July 9, 2014 - 14:58

Carole Goble will be presenting SEEK at the 15th Annual Bioinformatics Open Source Conference (BOSC 2014) in Boston, US.

The talk is at 14:00 on July 12th as part of the Open Science and Reproducible Research session. Entitled SEEK for Science: A Data Management Platform which Supports Open and Reproducible Science it will cover how SEEK is being customised and adopted to support open research in science.

For more information about BOSC please visit http://www.open-bio.org/wiki/BOSC_2014

There will also be a poster:



Monday, July 7, 2014 - 16:50

10 Simple Rules for the Care and Feeding of Scientific Data

Alyssa Goodman, Alberto Pepe, Alexander W. Blocker, Christine L. Borgman, Kyle Cranmer, Mercè Crosas, Rosanne Di Stefano, Yolanda Gil, Paul Groth, Margaret Hedstrom, David W. Hogg, Vinay Kashyap, Ashish Mahabal, Aneta Siemiginowska, Aleksandra Slavkovic

This article offers a short guide to the steps scientists can take to ensure that their data and associated analyses continue to be of value and to be recognized. In just the past few years, hundreds of scholarly papers and reports have been written on questions of data sharing, data provenance, research reproducibility, licensing, attribution, privacy, and more--but our goal here is not to review that literature. Instead, we present a short guide intended for researchers who want to know why it is important to "care for and feed" data, with some practical advice on how to do that. The set of Appendices at the close of this work offer links to the types of services referred to throughout the text. Boldface lettering below highlights actions one can take to follow the suggested rules.

https://www.authorea.com/users/3/articles/3410/_show_article

Friday, May 16, 2014 - 17:45

Please register for the 7th Berlin Summer Meeting: From Systems Biology to Systems Medicine NOW via the website http://www.berlinsummermeeting.org.

Abstract and poster submission is possible until May 17, registration (late) is possible until shortly before the meeting!

Tuesday, February 11, 2014 - 16:46

10th Annual International Symposium on Integrative Bioinformatics will be held in Newcastle, United Kingdom, from the 12th to 14th May 2014.


Current high throughput genomics technologies generate large quantities of high dimensional data. Biological data are scattered across thousands of biological databases and hundreds of scientific journals. The challenge for Integrative Bioinformatics in the e-Science age is to capture, model, integrate and analyse these data in order to provide systematic insights into complex biological systems.


This tenth meeting on Integrative Bioinformatics will be of interest to Bioinformaticians, Computer Scientists, Systems Biologists, Synthetic Biologists and others working or interested in the developing area of integrative bioinformatics. The meeting will provide an excellent environment and a range of opportunities to present and discuss methods, theoretical approaches, and their practical applications.

For more details please visit http://www.imbio.de/ib2014/

Wednesday, January 15, 2014 - 12:59

Within the SEEK team we are extremely proud to be able to congratulate Professor Carole Goble who has been awarded a CBE (Commander of the Order of the British Empire) for services to science. She was awarded this in the 2014 New Years Honours list.

Within the UK, this is a prestigious award selected by the Government for whom they feel have provided a significant contribution to society. CBE falls above the lesser awards of OBE (Officer of the Order of the British Empire) and MBE (Member of the Order of the British Empire). More details about this award and its history can be found at http://en.wikipedia.org/wiki/Order_of_the_British_Empire

Carole will be presented with the award by Queen Elizabeth II, and be provided with a particularly impressive looking medal.

Well done Carole, and we all feel it is very much deserved.

Wednesday, December 11, 2013 - 16:28

Application Deadline: February 15 2014

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, cell, tissue, organ and
network level using computational and biochemical methods.

The Synthetic and Systems Biology Summer School (SSBSS) is a
full-immersion course on cutting-edge advances in systems and
synthetic biology with lectures delivered by world-renowned experts.
The school provides a stimulating environment for doctoral students,
early career researches and industry leaders. Participants will also
have the chance to present their results (Oral presentations or
Posters) and to interact with their peers.

List of Speakers

  • Uri Alon, Weizmann Institute of Science, Israel
  • Jef Boeke, Johns Hopkins University, USA
  • Jason Chin, MRC Laboratory of Molecular Biology, UK
  • Virginia Cornish, Columbia University, USA
  • Angela DePace, Harvard University, USA
  • Paul Freemont, Imperial College London, UK
  • Farren Isaacs, Yale University, USA
  • Tanja Kortemme, University of California San Francisco, USA
  • Giuseppe Nicosia, University of Catania, Italy
  • Sven Panke, ETH, Switzerland
  • Rahul Sarpeshkar, MIT, USA
  • Giovanni Stracquadanio, Johns Hopkins University, USA
  • Ron Weiss, MIT, USA

Other speakers will be announced soon.

School Directors

  • Jef Boeke, Johns Hopkins University, USA
  • Giuseppe Nicosia, University of Catania, Italy
  • Mario Pavone, University of Catania, Italy
  • Giovanni Stracquadanio, Johns Hopkins University, USA

Short Talk and Poster Submission

Students may submit a research abstract for presentation. School
directors will review the abstracts and will recommend for poster or
short-oral presentation. Abstract should be submitted by February 15,
2014. The abstracts will be published on the electronic hands-out
material of the summer school.

For more details:

Web: http://www.taosciences.it/ssbss2014/
Email: ssbss2014@dmi.unict.it

Tuesday, November 12, 2013 - 15:40

Carole Goble presented a well received talk about SEEK and RightField at the International Semantic Web Conference (ISWC) in Sydney. The talk was about the use of RDF and Semantics in SEEK for Systems Biology, and had the title "Semantic Data and Models Sharing in systems Biology: The Just Enough Results Model and the SEEK Platform"

The slides for this talk are available online at http://www.seek4science.org/presentations