Presentations

Presentation of JERM templates at SEEK Users WS 2012 in Berlin (Olga Krebs)

Creator: Olga Krebs

Contributor: Olga Krebs

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

Contributor: Katy Wolstencroft

Olga's presentation at SySMO PALs meeting 29 – 30 November 2012, Heidelberg

Creators: Olga Krebs, PALs

Contributor: Olga Krebs

Poster presented during the ICSB 2011 conference in Mannheim

Creators: Abeer Fadda, Christine Clayton

Contributor: Abeer Fadda

Issues and considerations for data management as SysMO projects approach the end of their funding

Creator: Katy Wolstencroft

Contributor: Katy Wolstencroft

No description specified

Creator: Nadine Veith

Contributor: Nadine Veith

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

Contributor: Ulf Liebal

The talk shows that proline biosynthesis and accumulation is connected to glycine betaine availability. Glycine betaine complements proline function.

Creator: Tamara Hoffmann

Contributor: Ulf Liebal

December, 22th, 2011

Creator: Daniel Hönicke

Contributor: Daniel Hönicke

July, 8th, 2011

Creator: Daniel Hönicke

Contributor: Daniel Hönicke

April, 5th, 2011

Creator: Daniel Hönicke

Contributor: Daniel Hönicke

No description specified

Creator: Sebastian Curth

Contributor: Sebastian Curth

Presented by MARTIN SCHARM at SySMO PALs meeting 29-30 November 2012 in Heidelberg

Creators: Olga Krebs, MARTIN SCHARM

Contributor: Olga Krebs

Presentation given by Colin Harwood presenting results about ITC experiments to confirm interactions. Preliminary crystallisation experiments commenced on suitable candidates.

Creator: Colin Harwood

Contributor: Ulf Liebal

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

Contributor: Thomas Millat

No description specified

Creator: Thomas Rimpf

Contributor: Thomas Rimpf

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

Contributor: Stefan Henrich

No description specified

Creators: Thomas Millat, Ulf Liebal

Contributor: Thomas Millat

HITS/MCM Presentation at the SysMO-LAB2 meeting in Copenhagen on November, 22.11.2012

Creator: Stefan Henrich

Contributor: Stefan Henrich

No description specified

Creator: Tomas Fiedler

Contributor: Tomas Fiedler

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

Contributor: Ulf Liebal

Oral presentation given at ICSB 2011 in Mannheim/Heidelberg

Creator: Eduard Kerkhoven

Contributor: Eduard Kerkhoven

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

Contributor: Ulf Liebal

Presented by Ron Henkel at SySMO PALs meeting 29-30 November 2012 in Heidelberg

Creator: Ron Henkel

Contributor: Olga Krebs

No description specified

Creator: Thomas Rimpf

Contributor: Thomas Rimpf

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

Contributor: Stuart Owen

Presentation of JERM and new Master templates by Olga Krebs at SySMO PALs meeting in Heidelberg on 27th of August 2011

Creator: Olga Krebs

Contributor: Olga Krebs

Talk given by Olga Krebs at SysMO PALs meeting on 18 - 20 September 2013 in Paris

Creator: Olga Krebs

Contributor: Olga Krebs

Presented by Olga Krebs at All Hands PALs meeting on 21-22 of May 2012 in Warnemünde/Rostock

Creator: Olga Krebs

Contributor: Olga Krebs

No description specified

Creator: Thomas Rimpf

Contributor: Thomas Rimpf

No description specified

Creator: Thomas Rimpf

Contributor: Thomas Rimpf

No description specified

Creator: Wayne Aubrey

Contributor: Wayne Aubrey

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

Contributor: Thomas Millat

Presentation by Michael Ederer and Klaas Hellingwerf at the SysMO Conference 2013 (Feb 2013, Berlin)

Creator: Michael Ederer

Contributor: Michael Ederer

Talk given by Maksim Zakhartsev (Hohenheim University, Stuttgart, Germany, member of MOSES, ZucAt and ExtremoPharm projects)

Creator: Maksim Zakhartsev

Contributor: Maksim Zakhartsev

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

Contributor: Olga Krebs

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

Contributor: Stuart Owen

Presented at the annual PALs meeting in Rostock

Creator: Stuart Owen

Contributor: Stuart Owen

September, 13th, 2012

Creator: Daniel Hönicke

Contributor: Daniel Hönicke

This document is a summary of the SysMO-DB PALs meeting on the 29-30 November 2012

Creators: Katy Wolstencroft, Olga Krebs, Stuart Owen

Contributor: Katy Wolstencroft

No description specified

Creators: John Raedts, Servé Kengen

Contributor: John Raedts

No description specified

Creator: Armin Ehrenreich

Contributor: Sebastian Curth

No description specified

Creator: Christine Voigt

Contributor: Sebastian Curth

No description specified

Creator: Graeme Thorn

Contributor: Sebastian Curth

No description specified

Creator: Krzysztof Gizynski

Contributor: Sebastian Curth

No description specified

Creator: Sebastian Curth

Contributor: Sebastian Curth

No description specified

Creator: Servé Kengen

Contributor: Sebastian Curth

No description specified

Creator: Margrete Solheim

Contributor: Margrete Solheim

No description specified

Creators: None

Contributor: Sebastian Curth

Presentation on project progress - meeting Berlin April 5th 2012

Creator: John Raedts

Contributor: John Raedts

No description specified

Creator: Nadine Veith

Contributor: Nadine Veith

No description specified

Creator: Jacky Snoep

Contributor: Jacky Snoep

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

Contributor: Botond Cseke

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

Contributor: 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

Contributor: 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

Contributor: Olga Krebs

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

Contributor: Stuart Owen

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

Contributor: Olga Krebs

SEEK presentation at COMBINE meeting on 18th of August (by Olga Krebs)

Creators: None

Contributor: 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

Contributor: Stuart Owen

An overview of the SEEK for the HCLS Systems Biology Task force meeting

Creators: Katy Wolstencroft, Stuart Owen

Contributor: Katy Wolstencroft

No description specified

Creator: Quyen Nguyen

Contributor: Quyen Nguyen

No description specified

Creator: Quyen Nguyen

Contributor: Quyen Nguyen

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

Contributor: Stuart Owen

Katy Wolstencroft's talk at the "3rd Eagle Genomics Symposium:Will Big Data and Bigger Cuts Cripple Bioinformatics?", presented on 21st March 2013.

http://www.eaglegenomics.com/2013/01/eagles-third-symposium-how-the-efficient-bioinformatician-reduces-rd-costs/

Creator: Katy Wolstencroft

Contributor: Stuart Owen

Carole Goble's presentation at the SysMO Evaluation conference in Tenerife - May 2012.

Creator: Carole Goble

Contributor: 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

Contributor: Stuart Owen

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

Contributor: Anette McLeod

Presentation by Robert Pool at the SysMO Conference (Feb 2013 in Berlin)

Creator: Robert Poole

Contributor: Michael Ederer

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

Contributor: Franco Du Preez

Carole Goble's KeyNote talk at the 9th Intl Symp on Integrative Bioinformatics 2013 from the 20th Martch 2013

Creator: Carole Goble

Contributor: 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

Contributor: Thomas Millat

Poster presented during the ICSB 2011 conference in Mannheim

Creators: Alejandro Leroux, Luise Krauth-Siegel

Contributor: Alejandro Leroux

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

Contributor: Ulf Liebal

No description specified

Creator: Praveen Kumar Sappa

Contributor: Praveen Kumar Sappa

SysMO-LAB2 meeting in Copenhagen Nov 21-22, 2012

Creator: Jennifer Levering

Contributor: Jennifer Levering

Koen van Grinsven

Creator: Koen Van Grinsven

Contributor: Koen Van Grinsven

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

Contributor: Ulf Liebal

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