Presentations

128 Presentations visible to you, out of a total of 425

Poster presented at SWAT4LS - Semantic web applications and tools for life science- in Berlin at 10 of december 2014 by Olga Krebs

Creators: Olga Krebs, Carole Goble, Bernd Rinn, Wolfgang Müller, Quyen Nguyen, Jacky Snoep, Stuart Owen, Natalie Stanford, Peter Kunszt

Contributor: Olga Krebs

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

Creator: Olga Krebs

Contributor: Olga Krebs

Presented by Yannick Wurm at the first FAIRDOM user meeting.

Creators: Natalie Stanford, Yannick Wurm

Contributor: Natalie Stanford

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

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

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

Creators: Olga Krebs, MARTIN SCHARM

Contributor: Olga Krebs

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

Written and presented by Mihai Glont (EMBL-EBI, UK), at the Reproducible and Citable Data and Model Workshop, September 14th -16th 2015.

Creators: Natalie Stanford, Mihai Glont (EMBL-EBI, UK)

Contributor: Natalie Stanford

No description specified

Creator: Alexey Kolodkin

Contributor: Alexey Kolodkin

Prepared and presented by Jo McEntyre (EMBL_EBI) as part of the Reproducible and Citable Data and Models Workshop in Warnemünde, Germany. September 14th - 16th 2015.

Creators: Natalie Stanford, Jo McEntyre (EMBL_EBI)

Contributor: Natalie Stanford

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

Improve project deployment by letting your team focus on code quality instead of fixes problems. Spend more time on new features and let your project progress getting tested automatically.

Creator: Wout Van Helvoirt

Contributor: Wout Van Helvoirt

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

No description specified

Creator: Thomas Rimpf

Contributor: Thomas Rimpf

Carole Goble's talk at ERASysAPP - EXCHANGE Networking and Info Day for research projects of the first ERASysAPP call (a day before PALs meeting)

Creators: Olga Krebs, Carole Goble, Wolfgang Müller, Peter Kunszt, Bernd Rinn, Stuart Owen, Natalie Stanford, Jacky Snoep

Contributor: Olga Krebs

Presentation at the 10th anniversary of SABIO-RK, Heidelberg 2016

Creator: Dagmar Waltemath

Contributor: Dagmar Waltemath

Talk by Jon Olav Vik, Norwegian University of Life Sciences

Creator: Jon Olav Vik

Contributor: Olga Krebs

No description specified

Creator: Stephan Christel

Contributor: Stephan Christel

No description specified

Creator: Stephan Christel

Contributor: Stephan Christel

No description specified

Creator: Stephan Christel

Contributor: Stephan Christel

No description specified

Creator: Stephan Christel

Contributor: Stephan Christel

about Mark

Creator: Stephan Christel

Contributor: Stephan Christel

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

Talk given by Tomasz Zieliński

Creator: Tomasz Zielinski

Contributor: Olga Krebs

Oral presentation given at ICSB 2011 in Mannheim/Heidelberg

Creator: Eduard Kerkhoven

Contributor: Eduard Kerkhoven

Written and presented by Carole Goble (University of Manchester) at Multiscale Biology Network Springboard meeting, Nottingham. June 1st 2015.

Creators: Natalie Stanford, Carole Goble

Contributor: Natalie Stanford

Written and presented by Carole Goble (University of Manchester) at Multiscale Biology Network Springboard meeting, Nottingham. June 1st 2015.

Creators: Natalie Stanford, Carole Goble

Contributor: Natalie Stanford

Presentation of data management concepts for ERASysAPP projects at IMOMESIC kick off meeting on 8 th of May 2015 in Heidelberg. Part I presented by Olga Krebs

Creators: Olga Krebs, Caterina Barillari, Carole Goble, Peter Kunszt, Rostyslav Kuzyakiv, Wolfgang Müller, Quyen Nguyen, Stuart Owen, Bernd Rinn, Jacky Snoep, Natalie Stanford, Jakub Straszewski

Contributor: Olga Krebs

FAIRDOM Introduction

Creators: Natalie Stanford, Carole Goble

Contributor: Natalie Stanford

Documentation for using FAIRDOMHUB / SEEK for a workshop in Warnemunde, September 2015.

Creators: Natalie Stanford, Stuart Owen, Norman Morrison, Olga Krebs

Contributor: Natalie Stanford

No description specified

Creators: Olga Krebs, Stuart Owen, Caterina Barillari, Natalie Stanford, Rostyslav Kuzyakiv

Contributor: Olga Krebs

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

This document helps Horizon 2020 beneficiaries make their research data findable, accessible, interoperable and reusable (FAIR), to ensure it is soundly managed. Good research data management is not a goal in itself, but rather the key conduit leading to knowledge discovery and innovation, and to subsequent data and knowledge integration and reuse. Note that these guidelines do not apply to their full extent to actions funded by the ERC. For information and guidance concerning Open Access and the
...

Creator: Olga Krebs

Contributor: Olga Krebs

Here you find the Tasks for todays Hands-on Model Management in SEEK session

Creators: Ron Henkel, Dagmar Waltemath

Contributor: Ron Henkel

The paper by Tyson for the Hands-on Model Management in SEEK. Please refer to the related task sheet: https://fairdomhub.org/presentations/251

Creators: Ron Henkel, Dagmar Waltemath

Contributor: Ron Henkel

Hint Task 4. Please refer to the related task sheet: https://fairdomhub.org/presentations/251

Creators: Ron Henkel, Dagmar Waltemath

Contributor: Ron Henkel

Hint Task 5. Please refer to the related task sheet: https://fairdomhub.org/presentations/251

Creators: Ron Henkel, Dagmar Waltemath

Contributor: Ron Henkel

Hint Task 9A. Please refer to the related task sheet: https://fairdomhub.org/presentations/251

Creators: Ron Henkel, Dagmar Waltemath

Contributor: Ron Henkel

Hint Task 9. Please refer to the related task sheet: https://fairdomhub.org/presentations/251

Creators: Ron Henkel, Dagmar Waltemath

Contributor: Ron Henkel

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

Written by Martin Scharm (University of Rostock), Ron Henkel (University of Rostock), Dagmar Waltemath (University of Rostock), Olaf Wolkenhauer (University of Rostock, Stellenbosch University), and presented by Martin Scharm (University of Rostock) as part of the Reproducible and Citable Data and Models Workshop in Warnemünde, Germany. September 14th - 16th 2015.

Creators: Natalie Stanford, Dagmar Waltemath, Olaf Wolkenhauer, Ron Henkel, Martin Scharm (University of Rostock)

Contributor: Natalie Stanford

Step-by-step instructions for hands on session

Creator: Olga Krebs

Contributor: Olga Krebs

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

Prepared and presented by Carole Goble for the Reproducible and Citable Data and Models in Warnemünde, Germany. September 14th - 16th, 2015.

Creators: Natalie Stanford, Carole Goble

Contributor: Natalie Stanford

Written and presented by Wolfgang Müller (HITS) as part of the Reproducible and Citable Data and Models Workshop in Warnemünde, Germany. September 14th - 16th 2015.

Creators: Natalie Stanford, Wolfgang Müller

Contributor: Natalie Stanford

Our group develops computational models of the liver within the German systems biology projects VLN (Virtual Liver Network) and LiSyM (Systems Medicine of the Liver). In this talk we present our experiences in data and model management in recent years and future directions towards reproducible computational research we plan to implement.

We give an overview over the role of Fairdom and SEEK within our data management solution and how this integrates with and complements other approaches such as
...

Creator: Matthias König

Contributor: Matthias König

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

My graduation project presentation given on 22 of June at the Hanze University of Applied Sciences Groningen in The Netherlands.

Creator: Wout Van Helvoirt

Contributor: Wout Van Helvoirt

No description specified

Creator: Melanie Stefan

Contributor: Melanie Stefan

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

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

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

September, 13th, 2012

Creator: Daniel Hönicke

Contributor: Daniel Hönicke

The presentation was given during the PALs meeting in Munich on Dec. 10th, 2015
It talks about openBIS, an open, distributed system for managing biological information.
The main goal of openBIS is to support biological research data workflows from the source (i.e. the measurement instruments) to data processing and analyzing facilities.

Creator: Rostyslav Kuzyakiv

Contributor: Rostyslav Kuzyakiv

Report about PAL experience and data management solutions in MM-PLF LiSyM.

Creator: Matthias König

Contributor: Matthias König

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

Presented by Martin Böhm, German Cancer Research Center, Heidelberg, Germany

Creators: Markus Stepath, Martin Böhm

Contributor: Olga Krebs

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

Koen van Grinsven

Creator: Koen Van Grinsven

Contributor: Koen Van Grinsven

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: Alexey Kolodkin

Contributor: Alexey Kolodkin

Written and presented by Tom Ingraham (F1000), at the Reproducible and Citable Data and Model Workshop, in Warnemünde, Germany. September 14th -16th 2015.

Creators: Natalie Stanford, Tom Ingraham (F1000)

Contributor: Natalie Stanford

Talk by Jacky Snoep, Stellenbosch University, SA

Creator: Jacky Snoep

Contributor: Olga Krebs

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

Written and presented by Dagmar Waltemath (University of Rostock) as part of the Reproducible and Citable Data and Models Workshop in Warnemünde, Germany. September 14th - 16th 2015.

Creators: Natalie Stanford, Dagmar Waltemath

Contributor: Natalie Stanford

Workshop by the fairdomhub team on reproducible and citable data and models

Creator: Antoine Buetti-Dinh

Contributor: Antoine Buetti-Dinh

Prepared and presented by Carole Goble (University of Manchester), Wolfgang Mueller (HITS), Dagmar Waltermath (University of Rostock), at the Reproducible and Citable Data and Models Workshop, Warnemünde, Germany. September 14th - 16th 2015.

Creators: Natalie Stanford, Wolfgang Müller, Carole Goble, Dagmar Waltemath

Contributor: Natalie Stanford

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

No description specified

Creator: Ulrike Wittig

Contributor: Ulrike Wittig

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

Slides that were presented alongside a SEEK demonstration at the EraSysApp PALS meeting in Munich - December 2015

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

No description specified

Creator: Quyen Nguyen

Contributor: Quyen Nguyen

No description specified

Creator: Quyen Nguyen

Contributor: Quyen Nguyen

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

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

Creators: Katy Wolstencroft, Stuart Owen

Contributor: Katy Wolstencroft

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

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

Stephan's poster for presentation at IBS 2015

Creator: Stephan Christel

Contributor: Stephan Christel

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

Written and presented by Carole Goble (University of Manchester) as part of the Reproducible and Citable Data and Models Workshop in Warnemünde, Germany. September 14th - 16th 2015.

Creators: Natalie Stanford, Carole Goble, Stuart Owen

Contributor: Natalie Stanford

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

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

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

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

Talk given by Sergey Lashin from Institute of Cytology and Genetics, Novosibirsk, Russia

Creators: Sergey Lashin, Alexandra Klimenko

Contributor: Olga Krebs

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