König, Matthias Gleeson, Padraig Golebiewski, Martin Gorochowski, Thomas E. Hucka, Michael Keating, Sarah M. Myers, Chris J. Nickerson, David P. Sommer, Björn Waltemath, Dagmar
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Published in
Journal of Integrative Bioinformatics
This special issue of the Journal of Integrative Bioinformatics contains updated specifications of COMBINE standards in systems and synthetic biology. The 2022 special issue presents three updates to the standards: CellML 2.0.1, SBML Level 3 Package: Spatial Processes, Version 1, Release 1, and Synthetic Biology Open Language (SBOL) Version 3.1.0. ...
Clerx, Michael Cooling, Michael T. Cooper, Jonathan Garny, Alan Moyle, Keri Nickerson, David P. Nielsen, Poul M. F. Sorby, Hugh
Published in
Journal of Integrative Bioinformatics
We present here CellML 2.0.1, an XML-based language for describing and exchanging mathematical models of physiological systems. MathML embedded in CellML documents is used to define the underlying mathematics of models. Models consist of a network of reusable components, each with variables and equations giving relationships between those variables...
Buecherl, Lukas Mitchell, Thomas Scott-Brown, James Vaidyanathan, Prashant Vidal, Gonzalo Baig, Hasan Bartley, Bryan Beal, Jacob Crowther, Matthew Fontanarrosa, Pedro
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Published in
Journal of Integrative Bioinformatics
Synthetic biology builds upon genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. When designing a synthetic system, synthetic biologists need to exchange information about multiple types of molecules, the intended behavior of the system, and actual experimental measurements...
Schaff, James C. Lakshminarayana, Anuradha Murphy, Robert F. Bergmann, Frank T. Funahashi, Akira Sullivan, Devin P. Smith, Lucian P.
Published in
Journal of Integrative Bioinformatics
While many biological processes can be modeled by abstracting away the space in which those processes occur, some modeling (particularly at the cellular level) requires space itself to be modeled, with processes happening not in well-mixed compartments, but spatially-defined compartments. The SBML Level 3 Core specification does not include an expl...
Takan, Savaş Allmer, Jens
Published in
Journal of Integrative Bioinformatics
Science has become a highly competitive undertaking concerning, for example, resources, positions, students, and publications. At the same time, the number of journals presenting scientific findings skyrockets while the knowledge increase per manuscript seems to be diminishing. Science has also become ever more dependent on computational analyses. ...
Al-Hameli, Bassam Abdo Alsewari, AbdulRahman A. Basurra, Shadi S. Bhogal, Jagdev Ali, Mohammed A. H.
Published in
Journal of Integrative Bioinformatics
Diagnosing diabetes early is critical as it helps patients live with the disease in a healthy way – through healthy eating, taking appropriate medical doses, and making patients more vigilant in their movements/activities to avoid wounds that are difficult to heal for diabetic patients. Data mining techniques are typically used to detect diabetes w...
Balaur, Irina Roy, Ludovic Touré, Vasundra Mazein, Alexander Auffray, Charles
Published in
Journal of Integrative Bioinformatics
Systems biology researchers need feasible solutions for editing and visualisation of large biological diagrams. Here, we present the ySBGN bidirectional converter that translates metabolic pathways, developed in the general-purpose yEd Graph Editor (using the GraphML format) into the Systems Biology Graphical Notation Markup Language (SBGN-ML) stan...
Schilling, Marcel P. Schmelzer, Svenja Klinger, Lukas Reischl, Markus
Published in
Journal of Integrative Bioinformatics
Deep learning models achieve high-quality results in image processing. However, to robustly optimize parameters of deep neural networks, large annotated datasets are needed. Image annotation is often performed manually by experts without a comprehensive tool for assistance which is time- consuming, burdensome, and not intuitive. Using the here pres...
Wolff, Justus Matschinske, Julian Baumgart, Dietrich Pytlik, Anne Keck, Andreas Natarajan, Arunakiry von Schacky, Claudio E. Pauling, Josch K. Baumbach, Jan
Published in
Journal of Integrative Bioinformatics
The implementation of Artificial Intelligence (AI) still faces significant hurdles and one key factor is the access to data. One approach that could support that is federated machine learning (FL) since it allows for privacy preserving data access. For this proof of concept, a prediction model for coronary artery calcification scores (CACS) has bee...
Boulaamane, Yassir Ibrahim, Mahmoud A. A. Britel, Mohammed Reda Maurady, Amal
Published in
Journal of Integrative Bioinformatics
Parkinson’s disease is considered the second most frequent neurodegenerative disease. It is described by the loss of dopaminergic neurons in the mid-brain. For many decades, L-DOPA has been considered as the gold standard for treating Parkinson’s disease motor symptoms, however, due to the decrease of efficacy, in the long run, there is an urgent n...
