Journal: BMC Systems Biology

Article Title: A model reduction method for biochemical reaction networks

doi: 10.1186/1752-0509-8-52

Figure Lengend Snippet: Schematic of the original and reduced yeast-glycolysis networks. The left-hand panel is a schematic representation of the yeast glycolysis model used for model reduction. The full model description and an explanation of all the abbreviations is found in . The right-hand panel represents the reduced model after deleting 5 complexes (F6P, P2G, P3G, G6P and PEP). The blue arrows in the two panels indicate external fluxes.

Article Snippet: We have submitted to Biomodels two SBML files corresponding to the original and the reduced yeast glycolysis models (submission identifiers MODEL1403250001 and MODEL1403250002 respectively).

Techniques:

Journal: BMC Systems Biology

Article Title: A model reduction method for biochemical reaction networks

doi: 10.1186/1752-0509-8-52

Figure Lengend Snippet: Reduction of the yeast glycolysis model. Left-hand panel: minimum error integral versus number of deleted complexes (we have taken T =1.5 min for the computation of the error integral). Right-hand panel: identity of the deleted complexes and their convergence times.

Article Snippet: We have submitted to Biomodels two SBML files corresponding to the original and the reduced yeast glycolysis models (submission identifiers MODEL1403250001 and MODEL1403250002 respectively).

Techniques:

Journal: BMC Systems Biology

Article Title: A model reduction method for biochemical reaction networks

doi: 10.1186/1752-0509-8-52

Figure Lengend Snippet: Comparison of concentration profiles of yeast-glycolysis metabolites between the full and reduced models.

Article Snippet: We have submitted to Biomodels two SBML files corresponding to the original and the reduced yeast glycolysis models (submission identifiers MODEL1403250001 and MODEL1403250002 respectively).

Techniques: Comparison, Concentration Assay

Journal: Computer methods in biomechanics and biomedical engineering

Article Title: Full Body Musculoskeletal Model for Simulations of Gait in Persons with Transtibial Amputation

doi: 10.1080/10255842.2022.2065630

Figure Lengend Snippet: Segment Mass Properties of OpenSim Model

Article Snippet: These body masses, centers of mass, and moments of inertia were input to the generic amputee OpenSim model files so that the mass properties of the model’s residual limb and prosthesis match best possible estimates of amputated limb mass properties ( , ).

Techniques:

Journal: Computer methods in biomechanics and biomedical engineering

Article Title: Full Body Musculoskeletal Model for Simulations of Gait in Persons with Transtibial Amputation

doi: 10.1080/10255842.2022.2065630

Figure Lengend Snippet: Final amputee musculoskeletal model for OpenSim

Article Snippet: These body masses, centers of mass, and moments of inertia were input to the generic amputee OpenSim model files so that the mass properties of the model’s residual limb and prosthesis match best possible estimates of amputated limb mass properties ( , ).

Techniques:

Journal: BMC Genomics

Article Title: PP2 gene family in Phyllostachys edulis : identification, characterization, and expression profiles

doi: 10.1186/s12864-024-11007-5

Figure Lengend Snippet: Phylogenetic analysis was performed on 163 predicted PP2 protein sequences from eight plant species. Each subfamily represented a distinct color. The prefixes Phe, Ola, Rgu, Rdi, Bam, Gan, At, and Osa were used to identify PP2 proteins from P. edulis , O. latifolia , R. guianensis , R. distichophylla , B. amplexicaulis , G. angustifolia , A. thaliana , and O. sativa , respectively. RAxML-NG on ACCESS (1.2.0) in CIPRES ( https://www.phylo.org/ ) was used to construct a maximum likelihood (ML) phylogenetic tree. Furthermore, TBtools v2.110 was used for visualization

Article Snippet: A hidden Markov model file of PP2 (PF14299) was obtained from the InterPro website ( https://www.ebi.ac.uk/interpro/ ).

Techniques: Construct

Journal: Briefings in Bioinformatics

Article Title: Notions of similarity for systems biology models

doi: 10.1093/bib/bbw090

Figure Lengend Snippet: Comparison of two models describing the cell division cycle. Two SBML encoded models, obtained from BioModels, are compared by different aspects. Both models stem from the same publication describing the cell division cycle . Each box represents an aspect and shows an excerpt of BIOMD0000000005 on the left and BIOMD0000000006 on the right side.

Article Snippet: Using the original model BIOMD0000000005 as a query, we can screen BioModels for similar models by using the semanticSBML tool.

Techniques: Comparison

Journal: Briefings in Bioinformatics

Article Title: Notions of similarity for systems biology models

doi: 10.1093/bib/bbw090

Figure Lengend Snippet: Time courses for BIOMD0000000005 ( A ) and BIOMD0000000006 ( B ). Both time courses (with a duration of 100 s) were generated with COPASI . Model parameters and initial conditions remain as encoded in the SBML-files obtained from BioModels.

Article Snippet: Using the original model BIOMD0000000005 as a query, we can screen BioModels for similar models by using the semanticSBML tool.

Techniques: Generated

Journal: Briefings in Bioinformatics

Article Title: Notions of similarity for systems biology models

doi: 10.1093/bib/bbw090

Figure Lengend Snippet: Graph edit distance. To transform the network of BIOMD0000000005 into the network of BIOMD0000000006, 28 edit operations had to be performed; 16 edges and 11 nodes are deleted, 1 edge is inserted. Deletions are shown in red, insertions in blue and unchanged elements in grey. The node ∅, representing the empty set, is displayed multiple times for clarity.

Article Snippet: Using the original model BIOMD0000000005 as a query, we can screen BioModels for similar models by using the semanticSBML tool.

Techniques: