Presentations
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Talk given by Maksim Zakhartsev (Hohenheim University, Stuttgart, Germany, member of MOSES, ZucAt and ExtremoPharm projects)
Creator: Maksim Zakhartsev
Submitter: Maksim Zakhartsev
Presentation at the SysMO-LAB2 meeting in Copenhagen November 2012. Group from Nofima/Norwegian University of Life Sciences, Ås, Norway. Work on four strains of Lactobacillus plantarum, omics-analyses, diversity.
Creators: Anette McLeod, Lars Axelsson
Submitter: Anette McLeod
SysMO-LAB2 meeting in Copenhagen Nov 21-22, 2012
Creator: Jennifer Levering
Submitter: Jennifer Levering
HITS/MCM Presentation at the SysMO-LAB2 meeting in Copenhagen on November, 22.11.2012
Creator: Stefan Henrich
Submitter: Stefan Henrich
Poster presented at the 12th International Conference on Systems Biology (ICSB), Heidelberg/Mannheim, August 28 - September 1, 2011.
Creators: Stefan Henrich, Rebecca Wade, Anna Feldman-Salit, Nadine Veith
Submitter: Stefan Henrich
The second half of the overview of recent SEEK updates presented and discussed at the PALS meeting in Paris 2013. It is mostly covering infrastructure changes and also the addition of ORCID (http://orcid.org) support.
Creator: Stuart Owen
Submitter: Stuart Owen
Carole Goble's KeyNote talk at the 9th Intl Symp on Integrative Bioinformatics 2013 from the 20th Martch 2013
Creator: Carole Goble
Submitter: Stuart Owen
An overview of the JWS Online system, with emphasis on the latest model simulation interface and an update on the SBGN-ML and SED-ML support currently under development.
Creator: Martin Golebiewski
Submitter: Franco du Preez
SEEK presentation at COMBINE meeting on 18th of August (by Olga Krebs)
Creators: None
Submitter: Olga Krebs
Keynote presentation by Professor Carole Goble at BOSC (Bioinformatics Open Source Conference) Long Beach, California, USA, July 14 2012. Co-located with ISMB, Intelligent Systems in Molecular Biology
Also available on slideshare at http://www.slideshare.net/mygrid/if-we-build-it-will-they-come-13652794
Creator: Carole Goble
Submitter: Stuart Owen
Presentation by Carole Goble at the International Semantic Web Conference 2013 in Sydney Australia about the use of semantic web technology in SEEK and RightField.
Creators: Stuart Owen, Carole Goble, Katy Wolstencroft, Jacky Snoep, Wolfgang Müller, Olga Krebs, Quyen Nguyen
Submitter: Stuart Owen
Poster presented during the ICSB 2011 conference in Mannheim
Creators: Alejandro Leroux, Luise Krauth-Siegel
Submitter: Alejandro Leroux
Introduction to RightField and Demo were presented at the Virtual Liver Network PALs meeting on 31st of October in Hünfeld, Germany
Creators: Olga Krebs, Stuart Owen, Katy Wolstencroft
Submitter: Olga Krebs
Talk given by Olga Krebs at SysMO PALs meeting on 18 - 20 September 2013 in Paris
Creator: Olga Krebs
Submitter: Olga Krebs
Katy Wolstencroft's talk at the "3rd Eagle Genomics Symposium:Will Big Data and Bigger Cuts Cripple Bioinformatics?", presented on 21st March 2013.
Creator: Katy Wolstencroft
Submitter: Stuart Owen
The talk presented by Carole Goble and Wolfgang Mueller at the SysMO evaluation conference 2013 in Berlin.
Creators: Stuart Owen, Carole Goble, Wolfgang Müller
Submitter: Stuart Owen
This presentation reports about the results from an investigation of a ClosTron-mutant lacking CoA-transferase activity. Using our two-population model developed for the wild type of C. acetobutylicum, we analyse the changes in the formation of products caused by that mutation. In particular, we focus on the investigation of the acid re-assimilation after the initiation of the pH shift. Our comparison of experimental data and simulation unravels that an CoA-independent re-assimilation mechanism ...
Creator: Thomas Millat
Submitter: Thomas Millat
Presentation by Michael Ederer and Klaas Hellingwerf at the SysMO Conference 2013 (Feb 2013, Berlin)
Creator: Michael Ederer
Submitter: Michael Ederer
Presentation by Robert Pool at the SysMO Conference (Feb 2013 in Berlin)
Creator: Robert Poole
Submitter: Michael Ederer
Summary 1.1 modifying TFinfer to model the TFs using ON/OFF switches (fast response model), 1.2 trying to infer metabolites effect using a joint gene-tf-metabolite model, 2 analysing aerbiosis data using a similar model, 3 clustering genes for extending the EC network to obtain better fits to the data (feedback loop).
Creator: Botond Cseke
Submitter: Botond Cseke
Presented by MARTIN SCHARM at SySMO PALs meeting 29-30 November 2012 in Heidelberg
Creators: Olga Krebs, MARTIN SCHARM
Submitter: Olga Krebs
An overview of the RDF work being done with SEEK, given at the PALs meeting, November 2012. It gives a high level explanation of what RDF is, why its useful and can be used for filtering and finding out information about the data in SEEK. This talk proceeded an interactive session where the PALs came up with 20 questions, to help us refine our model and prioritise what we describe.
Creator: Stuart Owen
Submitter: Stuart Owen
The acetone-butanol-ethanol (ABE) fermentation of Clostridium acetobutylicum attracts new attention because it provides a potential alternative for the synthesis of value added chemicals to petroleum and other fossil reserves. This fermentative metabolic process comprises two distinct metabolic states that differ in their product spectrum. Growing on starch or sugars the predominant fermentation products are acetate and butyrate during acidogenesis (high pH). In contrast, C. acetobutylicum produces ...
Creator: Thomas Millat
Submitter: Thomas Millat
This document is a summary of the SysMO-DB PALs meeting on the 29-30 November 2012
Creators: Katy Wolstencroft, Olga Krebs, Stuart Owen
Submitter: Katy Wolstencroft
Issues and considerations for data management as SysMO projects approach the end of their funding
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
Presented by Ron Henkel at SySMO PALs meeting 29-30 November 2012 in Heidelberg
Creator: Ron Henkel
Submitter: Olga Krebs
This talk was presented at the IEEE e-Science conference, Chicago, USA (8-12 October 2012). http://www.ci.uchicago.edu/escience2012/ It describes the latest developments in RightField for both semantic data annotation and extraction to RDF.
Creators: Katy Wolstencroft, Stuart Owen, Carole Goble
Submitter: Katy Wolstencroft
Presented by Tobias Czauderna from Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) in Gatersleben at the SysMO PALs Meeting Heidelberg,29-11-2012
Creators: Olga Krebs, Tobias Czauderna
Submitter: Olga Krebs
Olga's presentation at SySMO PALs meeting 29 – 30 November 2012, Heidelberg
Creators: Olga Krebs, PALs
Submitter: Olga Krebs
SEEK at ICSB 2012 (presented by Olga Krebs)
Creators: Olga Krebs, Katy Wolstencroft, Carole Goble, Wolfgang Müller, Quyen Nguyen, Stuart Owen, Jacky Snoep, Franco du Preez, Martin Golebiewski, Andreas Weidemann
Submitter: Olga Krebs
Carole Goble's presentation at the SysMO Evaluation conference in Tenerife - May 2012.
Creator: Carole Goble
Submitter: Stuart Owen
Presented by Olga Krebs at All Hands PALs meeting on 21-22 of May 2012 in Warnemünde/Rostock
Creator: Olga Krebs
Submitter: Olga Krebs
Presentation of JERM templates at SEEK Users WS 2012 in Berlin (Olga Krebs)
Creator: Olga Krebs
Submitter: Olga Krebs
An overview of the SEEK for the HCLS Systems Biology Task force meeting
Creators: Katy Wolstencroft, Stuart Owen
Submitter: Katy Wolstencroft
Presentation on project progress - meeting Berlin April 5th 2012
Creator: John Raedts
Submitter: John Raedts
This presentation gives an overview of the way we structure and share data in the SEEK using JERM templates, and how we use the ISA hierarchy of Investigations, Studies, and Assays to associate experiments and data sets together. These slides were presented at the SEEK Users meeting in Berlin 2012.
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
Slide for an overview of new, and future upcoming features being developed in SEEK - presented at the Berlin SEEK Users Meeting March 2012.
Creator: Stuart Owen
Submitter: Stuart Owen
This presentation given at the 5th International Beilstein Symposium presents the development of a model for the pH-induced shift in C. acetobutylicum. Starting from experimental information, the model construction and underlying assumptions are explained. Furthermore, the required additions to the metabolic and genetic network caused by the used experimentals setup are established.
The established metabolic and genetic model is compared to dynamic shift experiments starting at acidogenesis and ...
Creator: Thomas Millat
Submitter: Thomas Millat
Oral presentation given at ICSB 2011 in Mannheim/Heidelberg
Creator: Eduard Kerkhoven
Submitter: Eduard Kerkhoven
Presentation of JERM and new Master templates by Olga Krebs at SySMO PALs meeting in Heidelberg on 27th of August 2011
Creator: Olga Krebs
Submitter: Olga Krebs
The presentation of new features in SEEK at last PALs meeing in Heidelberg on 27th of August by David, Lihua and Quyen
Creator: Olga Krebs
Submitter: Olga Krebs
In the talk I show that an increase in the concentration of one of two channelling enzyme has no effect on the flux. In contrast a decrease in the concentration of one of two channelling enzymes has the same effect like a concentration decrease of both enzymes.
Creator: Ulf Liebal
Submitter: Ulf Liebal
Presentation given by Colin Harwood presenting results about ITC experiments to confirm interactions. Preliminary crystallisation experiments commenced on suitable candidates.
Creator: Colin Harwood
Submitter: Ulf Liebal
The talk shows that proline biosynthesis and accumulation is connected to glycine betaine availability. Glycine betaine complements proline function.
Creator: Tamara Hoffmann
Submitter: Ulf Liebal
The talk shows that position 153 in various glutamate-kinases regulates proline feed-back regulation. This difference is shown for ProB being proline sensitivie and ProJ being proline independent.
Creator: Adrienne Zaprasis
Submitter: Ulf Liebal
Michael Kohlstedt presented flux data as integrated output of cellular components. Moreover, proteomics and metabolomics data reveal significant changes in intracellular protein and metabolite level and osmoprotection (supplementing glycine betaine) creates a novel metabolic state.
Creator: Michael Kohlstedt
Submitter: Ulf Liebal
Presentation by Thomas Millat of a tool for automatized analysis of flow cytometry data. It allows characterisation of different growth modalities, statistical measures of mean and variance and estimation of population overlap all along with appropriate visualization.
Creator: Thomas Millat
Submitter: Ulf Liebal
Poster presented during the ICSB 2011 conference in Mannheim
Creators: Abeer Fadda, Christine Clayton
Submitter: Abeer Fadda
The image file represents the activation of sigB in response to glucose starvation. It was drawn alongside the model 'sigb-response_starvation_shakeflask'. Biomass catalyses the conversion of glucose to biomass, while a low glucose concentration will negatively affect cell viability (inverted shown in the figure, where Glc inhibits cell death). W (RsbW) can form dimers with sigB (B) and dimers and trimers with V (RsbV)(WV, WV2) and is able to phosphorylate V to VP. A high glucose concentration ...
Creator: Ulf Liebal
Submitter: Ulf Liebal