We present a tutorial on using Pycellerator for biomolecular simulations. Models are described in human readable (and editable) text files (UTF8 or ASCII) containing collections of reactions, assignments, initial conditions, function definitions, and rate constants. These models are then converted into a Python program that can optionally solve the system, e.g., as a system of differential equations using ODEINT, or be run by another program. The input language implements an extended version of the Cellerator arrow notation, including mass action, Hill functions, S-Systems, MWC, and reactions with user-defined kinetic laws. Simple flux balance analysis is also implemented. We will demonstrate the implementation and analysis of progressively more complex models, starting from simple mass action through indexed cascades. Pycellerator can be used as a library that is integrated into other programs, run as a command line program, or in iPython notebooks. It is implemented in Python 2.7 and available under an open source GPL license.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1007/978-1-4939-9102-0_1 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
The aerial epidermis is a major site of quinolizidine alkaloid biosynthesis in narrow-leafed lupin.
New Phytol
January 2025
Section for Plant Biochemistry and Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Frederiksberg, Denmark.
Lupins are promising protein crops that accumulate toxic quinolizidine alkaloids (QAs) in the seeds, complicating their end-use. QAs are synthesized in green organs (leaves, stems, and pods) and a subset of them is transported to the seeds during fruit development. The exact sites of biosynthesis and accumulation remain unknown; however, mesophyll cells have been proposed as sources, and epidermal cells as sinks.
View Article and Find Full Text PDFAn inherently discrete-time model based on the mass action law for a heterogeneous population.
Math Biosci Eng
December 2024
Institute of of Information Technology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159 Street, building 34, 02-776 Warsaw, Poland.
In this paper, we introduce and analyze a discrete-time model of an epidemic spread in a heterogeneous population. As the heterogeneous population, we define a population in which we have two groups which differ in a risk of getting infected: a low-risk group and a high-risk group. We construct our model without discretization of its continuous-time counterpart, which is not a common approach.
View Article and Find Full Text PDFExploring high molecular weight components in Tityus serrulatus venom.
Toxicon
January 2025
Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil. Electronic address:
Our study identified high-molecular-weight compounds from Tityus serrulatus venom (TsV), and most of them have not yet been well explored. TsV was fractionated using FPLC system with different columns, analyzed by SDS-PAGE, and characterized by MALDI-TOF/TOF. Our study showed that TsV contains several high-molecular-weight compounds, including CRISPs, metalloproteinase and hyaluronidase.
View Article and Find Full Text PDFPurification, characterization, and mechanistic studies of Gassericin GA-3.1: A novel class IIc bacteriocin produced by Lactobacillus gasseri LG145.
Int J Biol Macromol
January 2025
College of Engineering, China Agricultural University, Beijing 100083, China. Electronic address:
Bacteriocins, naturally derived antimicrobial peptides, are considered promising alternatives to traditional preservatives and antibiotics, particularly in food and medical applications. Despite extensive research on various bacteriocins, cyclic varieties remain understudied. This study introduces Gassericin GA-3.
View Article and Find Full Text PDFMore self-efficacy is associated with longitudinally higher health-related quality of life in mechanically ventilated COVID-19 ICU survivors: The prospective MaastrICCht cohort.
Nurs Crit Care
January 2025
Department of Intensive Care Medicine, Maastricht University Medical Centre+, Maastricht, The Netherlands.
Background: More self-efficacy leads to greater confidence in one's ability to perform actions to achieve treatment goals. Therefore, self-efficacy may affect patient recovery and health-related quality of life (HRQoL) after ICU discharge.
Aim: In a cohort of mechanically ventilated COVID-19 survivors, we examined the associations between self-efficacy at 3 months and HRQoL at 3, 12 and 24 months after discharge.
Want AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!