scholarly journals BioSANS: A Software Package for Symbolic and Numeric Biological Simulation

2021 ◽  
Author(s):  
Erickson Fajiculay ◽  
Chao-Ping Hsu
Keyword(s):  
Parameter Estimation ◽  
User Interface ◽  
Systems Biology ◽  
Graphical User Interface ◽  
Software Package ◽  
Input Method ◽  
Biochemical Systems ◽  
Kinetics And Dynamics ◽  
Systems Biology Markup Language ◽  
Biological Simulation

Modeling biochemical systems can provide insights into behaviors that are difficult to observe or understand. It requires software, programming, and understanding of the system to build a model and study it. Softwares exist for such systems biology modeling, but most support only certain types of modeling tasks. Desirable features including ease in preparing input, symbolic or analytical computation, parameter estimation, graphical user interface, and systems biology markup language (SBML) support are not seen concurrently in one software package. In this study, we developed a python-based software that supports these features, with both deterministic and stochastic propagations. The software can be used by graphical user interface, command line, or as a python import. We also developed a semi-programmable and intuitively easy topology input method for the biochemical reactions. We tested the software with semantic and stochastic SBML test cases. Tests on symbolic solution and parameter estimation were also included. The software we developed is reliable, well performing, convenient to use, and compliant with most of the SBML tests. So far it is the only systems biology software that supports symbolic, deterministic, and stochastic modeling in one package that also features parameter estimation and SBML support. This work offers a comprehensive set of tools and allows for better availability and accessibility for studying kinetics and dynamics in biochemical systems.

scholarly journals Development of a Software Package for Cattle Identification in Nigeria

2019 ◽  
Vol 23 (10) ◽  
pp. 1825-1828 ◽  
Author(s):  
R.W. Bello ◽  
S. Abubakar
Keyword(s):  
Data Analysis ◽  
User Interface ◽  
Graphical User Interface ◽  
Software Package ◽  
Smart Phone ◽  
Information Encoding ◽  
Software Application ◽  
Free Range ◽  
Encoding Method ◽  
Tools And Methods

Open grazing or free-range grazing is one of the methods employed by the Nigeria nomadic cattle herders to provide pasture for their cattle. This method of providing pasture for cattle comes with so many challenges among which are cow swapping, ownership disputes, rustling and cow intrusion to farmland. Some existing methods of guiding against these challenges are expensive, injurious, and unreliable to apply. The objective of this paper is to develop an enhanced and affordable software package for cow recognition and identification using a graphical user interface and information encoding method. Data analysis module with software application for the analysis of the generated code is proposed; the software application installed on a computer or smart-phone may be standalone or otherwise. Data about individual cow is digitally collected, coded and stored using necessary resources, tools, and methods. Moreover, by tagging individual cow with the generated code, and matching the code with the ones in the database using code reader, individual cow can be recognized and identified.Keywords: Open grazing; Free-range grazing; Nomadic herder; Cow identification; Pasture.

scholarly journals PEtab—Interoperable specification of parameter estimation problems in systems biology

2021 ◽  
Vol 17 (1) ◽  
pp. e1008646 ◽  
Author(s):  
Leonard Schmiester ◽  
Yannik Schälte ◽  
Frank T. Bergmann ◽  
Tacio Camba ◽  
Erika Dudkin ◽  
...  
Keyword(s):  
Experimental Data ◽  
Parameter Estimation ◽  
Systems Biology ◽  
Model Simulation ◽  
Markup Language ◽  
Observation Model ◽  
Modeling Studies ◽  
Estimation Problems ◽  
Systems Biology Markup Language

Reproducibility and reusability of the results of data-based modeling studies are essential. Yet, there has been—so far—no broadly supported format for the specification of parameter estimation problems in systems biology. Here, we introduce PEtab, a format which facilitates the specification of parameter estimation problems using Systems Biology Markup Language (SBML) models and a set of tab-separated value files describing the observation model and experimental data as well as parameters to be estimated. We already implemented PEtab support into eight well-established model simulation and parameter estimation toolboxes with hundreds of users in total. We provide a Python library for validation and modification of a PEtab problem and currently 20 example parameter estimation problems based on recent studies.

scholarly journals SraTailor: GUI software for visualizing high-throughput sequence read archives

2014 ◽  
Author(s):  
Shinya Oki ◽  
Kazumitsu Maehara ◽  
Yasuyuki Ohkawa ◽  
Chikara Meno
Keyword(s):  
User Interface ◽  
Data Processing ◽  
High Throughput ◽  
Graphical User Interface ◽  
Software Package ◽  
Sequence Data ◽  
Command Line ◽  
Accession Number ◽  
Wide Range

Raw high-throughput sequence data are deposited in public databases as SRAs (Sequence Read Archives) and are publically available to every researcher. However, in order to graphically visualize the sequence data of interest, the corresponding SRAs must be downloaded and converted into BigWig format through complicated command-line processing. This task requires users to possess skill with script languages and sequence data processing, a requirement that prevents a wide range of biologists from exploiting SRAs. To address these challenges, we developed SraTailor, a GUI (Graphical User Interface) software package that automatically converts an SRA into a BigWig-formatted file. Simplicity of use is one of the most notable features of SraTailor: entering an accession number of an SRA and clicking the mouse are the only steps required in order to obtain BigWig-formatted files and to graphically visualize the extents of reads at given loci. SraTailor is also able to make peak calls and files of other formats, and the software also accepts various command-line-like options. Therefore, this software makes SRAs fully exploitable by a wide range of biologists. SraTailor is freely available at http://www.dev.med.kyushu-u.ac.jp/sra_tailor/.

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