AI Article Synopsis
- SBML (Systems Biology Markup Language) is a standard format for sharing biochemical models, and the SBML Layout and Render package helps create pathway diagrams for these models.
- The new Python package SBMLDiagrams simplifies adding and retrieving layout information through an easy-to-use API and supports diagram rendering to formats like PNG and PDF.
- SBMLDiagrams is open-source under the MIT license, available for major platforms, and can be installed via pip from GitHub.
Article Abstract
Summary: The systems biology markup language (SBML) is an extensible standard format for exchanging biochemical models. One of the extensions for SBML is the SBML Layout and Render package. This allows modelers to describe a biochemical model as a pathway diagram. However, up to now, there has been little support to help users easily add and retrieve such information from SBML. In this application note, we describe a new Python package called SBMLDiagrams. This package allows a user to add a layout and render information or retrieve it using a straightforward Python API. The package uses skia-python to support the rendering of the diagrams, allowing export to commons formats such as PNG or PDF.
Availability And Implementation: SBMLDiagrams is publicly available and licensed under the liberal MIT open-source license. The package is available for all major platforms. The source code has been deposited at GitHub (github.com/sys-bio/SBMLDiagrams). Users can install the package using the standard pip installation mechanism: pip install SBMLDiagrams.
Supplementary Information: Supplementary data are available at Bioinformatics online.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9805581 | PMC |
| http://dx.doi.org/10.1093/bioinformatics/btac730 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Research on equipment layout of multi-layer circular manufacturing cell based on NSGA III.
PLoS One
December 2024
School of Intelligent Manufacturing, Panzhihua University, Panzhihua, Sichuan, P. R. China.
Article Synopsis
- The paper focuses on optimizing layouts for multi-layer circular manufacturing cells (MCMC), which have been overlooked compared to single-layer cells (SCMC).
- Existing approaches primarily use NSGA II, but due to MCMC's complexity with more objectives, this study proposes employing the NSGA III algorithm for better multi-objective optimization.
- Validation using data from a smart factory in Zhejiang, China, shows that NSGA III offers significantly better layout solutions, contributing to advancements in smart factory design and enhancing MCMC research methodologies.
Instant-SFH: Non-Iterative Sparse Fourier Holograms Using Perlin Noise.
Sensors (Basel)
November 2024
Department of Computer Science, University of Maryland, College Park, MD 20742, USA.
Article Synopsis
- - Holographic displays are a new tech for augmented and virtual reality, offering realistic 3D visuals with improved depth perception by using fewer holographic pixels for higher efficiency.
- - Current methods for creating images in holographic form are too slow, taking hundreds of milliseconds, which is not practical for real-time applications.
- - This paper introduces a faster, non-iterative method using Perlin noise that improves rendering speed by over 600 times while maintaining image quality, making it suitable for interactive content in AR and VR.
Temperature is an important control factor for biologics biomanufacturing in precision fermentation. Here, we explored a highly responsive low temperature-inducible genetic system (LowTempGAL) in the model yeast Saccharomyces cerevisiae. Two temperature biosensors, a heat-inducible degron and a heat-inducible protein aggregation domain, were used to regulate the GAL activator Gal4p, rendering the leaky LowTempGAL systems.
View Article and Find Full Text PDFResearch on depth measurement calibration of light field camera based on Gaussian fitting.
Sci Rep
April 2024
School of Energy and Power Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China.
Optical field imaging technology does not require a complicated optical path layout and thus reduces hardware costs. Given that only one single exposure of a single camera can obtain three-dimensional information, this paper proposes an improved calibration method for depth measurement based on the theoretical model of optical field imaging. Specifically, the calibration time can be reduced since the Gaussian fitting can reduce the number of refocused images used to obtain the optimal refocusing coefficient calibration.
View Article and Find Full Text PDFModeling benefits and tradeoffs of green infrastructure: Evaluating and extending parsimonious models for neighborhood stormwater planning.
Heliyon
March 2024
School of Public Policy and Urban Affairs, College of Social Sciences and Humanities, Northeastern University. 310 Renaissance Park, 1135 Tremont St, Boston, MA 02115, USA.
Green infrastructure is often proposed to complement conventional urban stormwater management systems that are stressed by extreme storms and expanding impervious surfaces. Established hydrological and hydraulic models inform stormwater engineering but are time- and data-intensive or aspatial, rendering them inadequate for rapid exploration of solutions. Simple spreadsheet models support quick site plan assessments but cannot adequately represent spatial interactions beyond a site.
View Article and Find Full Text PDFWant 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!