Back

Executable Simulation Model of the Liver

König, M.

2020-01-06 systems biology
10.1101/2020.01.04.894873 bioRxiv
Show abstract

To address the issue of reproducibility in computational modeling we developed the concept of an executable simulation model (EXSIMO). An EXSIMO combines model, data and code with the execution environment to run the computational analysis in an automated manner using tools from software engineering. Key components are i) models, data and code for the computational analysis; ii) tests for models, data and code; and iii) an automation layer to run tests and execute the analysis. An EXSIMO combines version control, model, data, units, annotations, analysis, reports, execution environment, testing, continuous integration and release. We applied the concept to perform a replication study of a computational analysis of hepatic glucose metabolism in the liver. The corresponding EXSIMO is available from https://github.com/matthiaskoenig/exsimo.

Matching journals

The top 4 journals account for 50% of the predicted probability mass.

1
Bioinformatics
◐ 1204 papers in training set
Top 1%
18.8%
Similar papers in this journal
2
PLOS Computational Biology
● 1863 papers in training set
Top 2%
15.3%
Similar papers in this journal
3
BMC Bioinformatics
○ 457 papers in training set
Top 0.2%
15.3%
Similar papers in this journal
4
PLOS ONE
● 5266 papers in training set
Top 19%
9.0%
Similar papers in this journal
50% of probability mass above
5
Bioinformatics Advances
◐ 203 papers in training set
Top 2%
3.3%
Similar papers in this journal
6
iScience
○ 1154 papers in training set
Top 6%
3.3%
7
Scientific Reports
○ 3612 papers in training set
Top 38%
2.7%
8
Computational and Structural Biotechnology Journal
● 242 papers in training set
Top 2%
2.4%
9
Gigabyte
● 62 papers in training set
Top 0.6%
1.8%
10
npj Systems Biology and Applications
○ 125 papers in training set
Top 0.9%
1.8%
11
eLife
● 5828 papers in training set
Top 53%
1.5%
12
Briefings in Bioinformatics
◐ 354 papers in training set
Top 5%
1.4%
13
Computer Methods and Programs in Biomedicine
○ 28 papers in training set
Top 0.7%
1.1%
14
Cell Reports Methods
○ 165 papers in training set
Top 2%
1.1%
15
GigaScience
◐ 212 papers in training set
Top 3%
1.1%
16
Metabolites
○ 53 papers in training set
Top 0.8%
1.0%
17
Frontiers in Bioengineering and Biotechnology
○ 98 papers in training set
Top 2%
0.9%
18
Frontiers in Systems Biology
○ 10 papers in training set
Top 0.1%
0.9%
19
Journal of Molecular Biology
○ 232 papers in training set
Top 4%
0.9%
20
Biomolecules
○ 100 papers in training set
Top 3%
0.6%
21
Nucleic Acids Research
◐ 1281 papers in training set
Top 14%
0.6%
22
Neuroinformatics
○ 46 papers in training set
Top 0.9%
0.6%
23
BMC Research Notes
○ 33 papers in training set
Top 1%
0.6%
24
Frontiers in Molecular Biosciences
○ 102 papers in training set
Top 3%
0.6%
25
Nature Communications
○ 5641 papers in training set
Top 58%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.