Moritz E. Beber
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In Pursuit of Total Reproducibility Open
The vast majority of scientific contributions in the field of computational systems biology are based on mathematical models. These models can be broadly classified as either dynamic (kinetic) models or steady-state (constraint-based) mode…
View article: FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models
FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models Open
Genome-scale metabolic models (GEMs) and other constraint-based models (CBMs) play a pivotal role in understanding biological phenotypes and advancing research in areas like metabolic engineering, human disease modelling, drug discovery, a…
nf-core/taxprofiler: highly parallelised and flexible pipeline for metagenomic taxonomic classification and profiling Open
1 Abstract Metagenomic classification tackles the problem of characterising the taxonomic source of all DNA sequencing reads in a sample. A common approach to address the differences and biases between the many different taxonomic classifi…
TAXPASTA: TAXonomic Profile Aggregation andSTAndardisation Open
Metagenomic analysis is largely concerned with untargeted genetic characterisation of the taxonomic and functional composition of whole communities of organisms.Researchers ask questions from metagenomic sequencing such as 'who is present'…
View article: BioSimulators: a central registry of simulation engines and services for recommending specific tools
BioSimulators: a central registry of simulation engines and services for recommending specific tools Open
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various …
View article: BioSimulators: a central registry of simulation engines and services for\n recommending specific tools
BioSimulators: a central registry of simulation engines and services for\n recommending specific tools Open
Computational models have great potential to accelerate bioscience,\nbioengineering, and medicine. However, it remains challenging to reproduce and\nreuse simulations, in part, because the numerous formats and methods for\nsimulating vario…
Long-Term Effects of a Web-Based Low-FODMAP Diet Versus Probiotic Treatment for Irritable Bowel Syndrome, Including Shotgun Analyses of Microbiota: Randomized, Double-Crossover Clinical Trial Open
Background The long-term management of irritable bowel syndrome (IBS) poses many challenges. In short-term studies, eHealth interventions have been demonstrated to be safe and practical for at-home monitoring of the effects of probiotic tr…
eQuilibrator 3.0: a database solution for thermodynamic constant estimation Open
eQuilibrator (equilibrator.weizmann.ac.il) is a database of biochemical equilibrium constants and Gibbs free energies, originally designed as a web-based interface. While the website now counts around 1,000 distinct monthly users, its desi…
multiTFA: a Python package for multi-variate thermodynamics-based flux analysis Open
Motivation We achieve a significant improvement in thermodynamic-based flux analysis (TFA) by introducing multivariate treatment of thermodynamic variables and leveraging component contribution, the state-of-the-art implementation of the g…
eQuilibrator 3.0 -- a platform for the estimation of thermodynamic constants Open
eQuilibrator (equilibrator.weizmann.ac.il) is a calculator for biochemical equilibrium constants and Gibbs free energies, originally designed as a web-based interface. While the website now counts ${\sim}1000$ distinct monthly users, its d…
multiTFA: a Python package for multi-variate Thermodynamics-based Flux Analysis Open
Summary We achieve a significant improvement in thermodynamic-based flux analysis (TFA) by introducing multivariate treatment of thermodynamic variables and leveraging component contribution, the state-of-the-art implementation of the grou…
View article: The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes Open
In the Abstract, the url https://modelseed.org has been replaced with https://modelseed.org/biochem.
Compound Database for eQuilibrator Open
An indexed database of compounds from the MetaNetX, reference database version 3.1. Structures are enriched with information using OpenBabel and ChemAxon.
Compound Database for eQuilibrator Open
An indexed database of compounds from the MetaNetX, reference database version 3.1. Structures are enriched with information using OpenBabel and ChemAxon.
Author Correction: A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism Open
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
View article: The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes Open
For over 10 years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. Now being released, the biochemistry database serves as the foundation of b…
View article: The ModelSEED Database for the integration of metabolic annotations and the reconstruction, comparison, and analysis of metabolic models for plants, fungi, and microbes
The ModelSEED Database for the integration of metabolic annotations and the reconstruction, comparison, and analysis of metabolic models for plants, fungi, and microbes Open
For over ten years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. Now being released, the biochemistry database serves as the foundation of …
Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing Open
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
MEMOTE for standardized genome-scale metabolic model testing Open
Reconstructing metabolic reaction networks enables the development of testable hypotheses of an organism’s metabolism under different conditions. State-of-the-art genome-scale metabolic models (GEMs) can include thousands of metabolites an…
biosustain/memote-meta-study: Supplementary Material Open
Test metabolic models in the wild and rank them according to popularity and how easily they can be improved.
biosustain/memote-meta-models: collection publication state Open
Freeze the model collection state as it was for the memote meta study.
Cameo: A Python Library for Computer Aided Metabolic Engineering and Optimization of Cell Factories Open
Computational systems biology methods enable rational design of cell factories on a genome-scale and thus accelerate the engineering of cells for the production of valuable chemicals and proteins. Unfortunately, the majority of these metho…
Cameo: A Python Library for Computer Aided Metabolic Engineering and Optimization of Cell Factories Open
Computational systems biology methods enable rational design of cell factories on a genomescale and thus accelerate the engineering of cells for the production of valuable chemicals and proteins. Unfortunately, for the majority of these me…
Interplay of digital and analog control in time-resolved gene expression profiles Open
Background\nMeasuring the agreement between a gene expression profile and a known transcriptional regulatory network is an important step in the functional interpretation of bacterial physiological state. In this way, general design princi…
Effect of database drift on network topology and enrichment analyses: a case study for RegulonDB Open
RegulonDB is a database storing the biological information behind the transcriptional regulatory network (TRN) of the bacterium Escherichia coli. It is one of the key bioinformatics resources for Systems Biology investigations of bacterial…