Evidence map›Paper›PMID 30218605›Full record

ArticleJournal of integrative bioinformatics2018

Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA.

Christoph Brinkrolf, Nadja A Henke, Lennart Ochel, Boas Pucker, Olaf Kruse, Petra Lutter

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of integrative bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Christoph BrinkrolfBielefeld University, Faculty of Technology, Bioinformatics Department, Bielefeld, Germany.
Nadja A HenkeBielefeld University, Faculty of Biology and CeBiTec, Genetics of Prokaryotes, Bielefeld, Germany.
Lennart OchelBielefeld University, Faculty of Technology, Bioinformatics Department, Bielefeld, Germany.
Boas PuckerBielefeld University, Faculty of Biology and CeBiTec, Genome Research, Bielefeld, Germany.
Olaf KruseBielefeld University, Faculty of Biology and CeBiTec, Algae Biotechnology and Bioenergy, Bielefeld, Germany.
Petra LutterBielefeld University, Faculty of Biology and CeBiTec, Proteome and Metabolome Research, Bielefeld, Germany.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

In this work we present new concepts of VANESA, a tool for modeling and simulation in systems biology. We provide a convenient way to handle mathematical expressions and take physical units into account. Simulation and result management has been improved, and syntax and consistency checks, based on physical units, reduce modeling errors. As a proof of concept, essential components of the aerobic carbon metabolism of the green microalga Chlamydomonas reinhardtii are modeled and simulated. The modeling process is based on xHPN Petri net formalism and simulation is performed with OpenModelica, a powerful environment and compiler for Modelica. VANESA, as well as OpenModelica, is open source, free-of-charge for non-commercial use, and is available at: http://agbi.techfak.uni-bielefeld.de/vanesa.

Indexed as

Computer SimulationMetabolic Networks and PathwaysSoftwareAlgorithmsCarbonChlamydomonas reinhardtiiModels, BiologicalWorkflowCarbonChlamydomonas reinhardtiimetabolic networkOpenModelicasystems biologyxHPN

Identifiers

PMID30218605
PMCPMC6340121

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.