FAIRDOM-SEEK Training

This paper explores key success factors for the development and implementation of a Common Data Model (CDM) for Rare Diseases (RDs) focusing on the European context. Several challenges hinder RD care …

Authors: A. S. L. Graefe, F. Rehburg, M. Hubner, S. Thun, O. Beyan

Date Published: 22nd Aug 2024

Publication Type: Proceedings

PubMed ID: 39176641

Citation: Stud Health Technol Inform. 2024 Aug 22;316:1396-1400. doi: 10.3233/SHTI240672.

Created: 26th Nov 2024 at 14:08

Metabolome plasticity in 241 Arabidopsis thaliana accessions reveals evolutionary cold adaptation processes.

Tools for Systems biology modeling and data exchange - training course 2023

Abstract (Expand)

Acclimation and adaptation of metabolism to a changing environment are key processes for plant survival and reproductive success. In the present study, 241 natural accessions of Arabidopsis (Arabidopsis …

Authors: J. Weiszmann, D. Walther, P. Clauw, G. Back, J. Gunis, I. Reichardt, S. Koemeda, J. Jez, M. Nordborg, J. Schwarzerova, I. Pierides, T. Nagele, W. Weckwerth

Date Published: 22nd Sep 2023

Publication Type: Journal

PubMed ID: 37220420

Citation: Plant Physiol. 2023 Sep 22;193(2):980-1000. doi: 10.1093/plphys/kiad298.

Created: 30th Nov 2023 at 12:44, Last updated: 30th Nov 2023 at 12:47

EnzymeML: seamless data flow and modeling of enzymatic data.

de.NBI Spring School

Abstract (Expand)

The design of biocatalytic reaction systems is highly complex owing to the dependency of the estimated kinetic parameters on the enzyme, the reaction conditions, and the modeling method. Consequently, …

Authors: S. Lauterbach, H. Dienhart, J. Range, S. Malzacher, J. D. Sporing, D. Rother, M. F. Pinto, P. Martins, C. E. Lagerman, A. S. Bommarius, A. V. Host, J. M. Woodley, S. Ngubane, T. Kudanga, F. T. Bergmann, J. M. Rohwer, D. Iglezakis, A. Weidemann, U. Wittig, C. Kettner, N. Swainston, S. Schnell, J. Pleiss

Date Published: 10th Feb 2023

Publication Type: Journal

PubMed ID: 36759590

Citation: Nat Methods. 2023 Mar;20(3):400-402. doi: 10.1038/s41592-022-01763-1. Epub 2023 Feb 9.

Created: 17th Mar 2023 at 11:35

Making Sense of "Nonsense" and More: Challenges and Opportunities in the Genetic Code Expansion, in the World of tRNA Modifications.

Workshop FAIRDOMHub / FAIRDOM-SEEK - training course 2024

Abstract (Expand)

The evolutional development of the RNA translation process that leads to protein synthesis based on naturally occurring amino acids has its continuation via synthetic biology, the so-called rational …

Authors: O. M. Lateef, M. O. Akintubosun, O. T. Olaoba, S. O. Samson, M. Adamczyk

Date Published: 15th Jan 2022

Publication Type: Journal

PubMed ID: 35055121

Citation: Int J Mol Sci. 2022 Jan 15;23(2):938. doi: 10.3390/ijms23020938.

Created: 26th Nov 2024 at 14:06

Keratinases as Versatile Enzymatic Tools for Sustainable Development

Workshop FAIRDOMHub / FAIRDOM-SEEK - training course 2024

Abstract (Expand)

To reduce anthropological pressure on the environment, the implementation of novel technologies in present and future economies is needed for sustainable development. The food industry, with dairy and …

Authors: Marcin Sypka, Iga Jodłowska, Aneta M. Białkowska

Date Published: 1st Dec 2021

Publication Type: Journal

DOI: 10.3390/biom11121900

Citation: Biomolecules 11(12):1900

Created: 26th Nov 2024 at 14:00, Last updated: 26th Nov 2024 at 14:04

Prediction and analysis of redox-sensitive cysteines using machine learning and statistical methods.

Tools for Systems biology modeling and data exchange - training course 2023

Abstract (Expand)

Reactive oxygen species are produced by a number of stimuli and can lead both to irreversible intracellular damage and signaling through reversible post-translational modification. It is unclear which …

Authors: M. Kessler, I. Wittig, J. Ackermann, I. Koch

Date Published: 27th Jul 2021

Publication Type: Journal

PubMed ID: 34261205

Citation: Biol Chem. 2021 Jan 6;402(8):925-935. doi: 10.1515/hsz-2020-0321. Print 2021 Jul 27.

Created: 30th Nov 2023 at 12:49

Solvent Selection in Homogeneous Catalysis—Optimization of Kinetics and Reaction Performance

Tools for Systems biology modeling and data exchange - training course 2023

Abstract

Not specified

Authors: Fabian Huxoll, Froze Jameel, Jonas Bianga, Thomas Seidensticker, Matthias Stein, Gabriele Sadowski, Dieter Vogt

Date Published: 15th Jan 2021

Publication Type: Journal

DOI: 10.1021/acscatal.0c04431

Citation: ACS Catal. 11(2):590-594

Created: 30th Nov 2023 at 13:13, Last updated: 30th Nov 2023 at 13:15

Chloroplast-Specific in Vivo Ca 2+ Imaging Using Yellow Cameleon Fluorescent Protein Sensors Reveals Organelle-Autonomous Ca 2+ Signatures in the Stroma

Tools for Systems biology modeling and data exchange - training course 2023

Abstract

Not specified

Authors: Giovanna Loro, Stephan Wagner, Fabrizio Gandolfo Doccula, Smrutisanjita Behera, Stefan Weinl, Joerg Kudla, Markus Schwarzländer, Alex Costa, Michela Zottini

Date Published: 2nd Aug 2016

Publication Type: Journal

DOI: 10.1104/pp.16.00652

Citation: Plant Physiol. 171(4):2317-2330

Created: 30th Nov 2023 at 13:02, Last updated: 30th Nov 2023 at 13:03

Pyruvate kinase: Function, regulation and role in cancer.

Workshop FAIRDOMHub / FAIRDOM-SEEK - training course 2024

Abstract (Expand)

Pyruvate kinase is an enzyme that catalyzes the conversion of phosphoenolpyruvate and ADP to pyruvate and ATP in glycolysis and plays a role in regulating cell metabolism. There are four mammalian …

Authors: W. J. Israelsen, M. G. Vander Heiden

Date Published: 17th Aug 2015

Publication Type: Journal

PubMed ID: 26277545

Citation: Semin Cell Dev Biol. 2015 Jul;43:43-51. doi: 10.1016/j.semcdb.2015.08.004. Epub 2015 Aug 13.

Created: 26th Nov 2024 at 10:35

The role of the anterior lateral eyes in the vision-based behaviour of jumping spiders

Workshop FAIRDOMHub / FAIRDOM-SEEK - training course 2024

Abstract (Expand)

SUMMARY Jumping spiders, or salticids, sample their environment using a combination of two types of eyes. The forward-facing pair of ‘principal’ eyes have narrow fields of view, but exceptional spatial …

Authors: Daniel B. Zurek, Alan J. Taylor, Christopher S. Evans, Ximena J. Nelson

Date Published: 15th Jul 2010

Publication Type: Journal

DOI: 10.1242/jeb.042382

Citation: Journal of Experimental Biology 213(14):2372-2378

Created: 26th Nov 2024 at 14:07, Last updated: 26th Nov 2024 at 14:08

The Synthesis Rates of Total Liver Protein and Plasma Albumin Determined Simultaneously In Vivo In Humans

Workshop FAIRDOMHub / FAIRDOM-SEEK - training course 2024

Abstract (Expand)

Although the metabolism of liver–derived plasma proteins such as albumin has been extensively studied, human hepatic protein synthesis as a whole has not been well characterized, because a reproducible …

Authors: H. Barle, B. Nyberg, P. Essén, K. Andersson, M. A. McNurlan, J. Wernerman, P. J. Garlick

Date Published: 1997

Publication Type: Journal

DOI: 10.1002/hep.510250128

Citation: Hepatology 25(1):154-158

Created: 26th Nov 2024 at 14:05, Last updated: 26th Nov 2024 at 14:07

A new granulation method for compressed tablets [proceedings].

de.NBI Spring School

Abstract

Not specified

Author: M. H. Rubinstein

Date Published: 1st Dec 1976

Publication Type: Journal

PubMed ID: 12345

Citation: J Pharm Pharmacol. 1976 Dec;28 Suppl:67P.

Created: 17th Mar 2023 at 11:22

A new granulation method for compressed tablets [proceedings].

Tools for Systems biology modeling and data exchange - training course 2023

Abstract

Not specified

Author: M. H. Rubinstein

Date Published: 1st Dec 1976

Publication Type: Journal

PubMed ID: 12345

Citation: J Pharm Pharmacol. 1976 Dec;28 Suppl:67P.

Created: 30th Nov 2023 at 12:40

Change in the kinetics of sulphacetamide tissue distribution in Walker tumor-bearing rats.

Tools for Systems biology modeling and data exchange - training course 2023

Abstract (Expand)

The effect of Walker tumor on sulphacetamide distribution was studied in rats 21 days after tumor implantation in a hind leg. After oral administration of sulphacetamide (5 and 20 min), the concentration …

Authors: D. Nadeau, C. Marchand

Date Published: 1st Nov 1975

Publication Type: Journal

PubMed ID: 1234

Citation: Drug Metab Dispos. 1975 Nov-Dec;3(6):565-76.

Created: 30th Nov 2023 at 12:46

Digitoxin metabolism by rat liver microsomes.

Tools for Systems biology modeling and data exchange - training course 2023

Abstract

Not specified

Authors: A. Schmoldt, H. F. Benthe, G. Haberland

Date Published: 1st Sep 1975

Publication Type: Journal

PubMed ID: 10

Citation: Biochem Pharmacol. 1975 Sep 1;24(17):1639-41.

Created: 30th Nov 2023 at 12:58

Digitoxin metabolism by rat liver microsomes.

Workshop FAIRDOMHub / FAIRDOM-SEEK - training course 2024

Abstract

Not specified

Authors: A. Schmoldt, H. F. Benthe, G. Haberland

Date Published: 1st Sep 1975

Publication Type: Journal

PubMed ID: 10

Citation: Biochem Pharmacol. 1975 Sep 1;24(17):1639-41.

Created: 26th Nov 2024 at 14:03

Thermodynamic parameters of reactions involving E. Coli, a review

Tools for Systems biology modeling and data exchange - training course 2023

Abstract

Not specified

Editor:

Date Published: No date defined

Publication Type: Journal

Citation:

Created: 30th Nov 2023 at 12:56

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FAIRDOM-SEEK Introduction

Tools for Systems biology modeling and data exchange - training course 2023

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Creator: Ulrike Wittig

Submitter: Ulrike Wittig

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Created: 30th Nov 2023 at 11:00

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Workshop FAIRDOMHub/FAIRDOM-SEEK 2024

FAIRDOMHub (https://fairdomhub.org/) is a free research data management platform built upon the FAIRDOM-SEEK software (http://fairdomseek.org). FAIRDOM-SEEK is an open source tool for uploading, organizing, sharing and publishing scientific research data. FAIRDOM-SEEK contains specific features for systems biologists for data and model management.

Agenda:

Introduction to FAIRDOMHub / FAIRDOM-SEEK
Hands-on session:
Storage and exchange of data and models according to the FAIR principles

...

Start Date: 26th Nov 2024 (26th Nov 2024 (Europe/Berlin))

End Date: 26th Nov 2024 (26th Nov 2024 (Europe/Berlin))

Event Website: http://denbi-modsim.de/workshop_2024/hits/

Country: Not specified

City: online event

Created: 20th Nov 2024 at 12:44, Last updated: 28th Nov 2024 at 08:45

Tools for systems biology modeling and data exchange

During this 3-day course, attendees will learn basic techniques for modeling of biochemical networks including data access and storage due to the FAIR principles. The first day introduces kinetic modeling techniques which will be illustrated and exercised with COPASI. The second day continues with principles of stoichiometric and constraint-based modeling coupled with hands on exercises using CellNetAnalyzer and a demonstration of CNApy. The third day SABIO-RK is used as a resource for kinetic ...

Start Date: 28th Nov 2023 (28th Nov 2023 (Etc/UTC))

End Date: 30th Nov 2023 (30th Nov 2023 (Etc/UTC))

Event Website: http://denbi-modsim.de/workshop_11-2023/

Country: Germany

City: Magdeburg

Created: 25th Jul 2022 at 09:37, Last updated: 30th Nov 2023 at 11:58

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