MatOpt: A Python Package for Nanomaterials Design Using Discrete Optimization

2022 ◽  
Author(s):  
Christopher L. Hanselman ◽  
Xiangyu Yin ◽  
David C. Miller ◽  
Chrysanthos E. Gounaris
Keyword(s):  
Discrete Optimization ◽  
Python Package

Discrete optimization of semi-rigid steel frames in second-order analysis

2019 ◽  
Author(s):  
Marcos Henrique Bossardi Borges ◽  
Adelano Esposito ◽  
Herbert Gomes
Keyword(s):  
Discrete Optimization ◽  
Steel Frames ◽  
Second Order ◽  
Order Analysis

scholarly journals pymia: A Python package for data handling and evaluation in deep learning-based medical image analysis

2021 ◽  
Vol 198 ◽  
pp. 105796
Author(s):  
Alain Jungo ◽  
Olivier Scheidegger ◽  
Mauricio Reyes ◽  
Fabian Balsiger
Keyword(s):  
Image Analysis ◽  
Deep Learning ◽  
Medical Image ◽  
Medical Image Analysis ◽  
Data Handling ◽  
Python Package

scholarly journals GriSPy: A Python package for fixed-radius nearest neighbors search

2020 ◽  
pp. 100443
Author(s):  
M. Chalela ◽  
E. Sillero ◽  
L. Pereyra ◽  
M.A. Garcia ◽  
J.B. Cabral ◽  
...  
Keyword(s):  
Nearest Neighbors ◽  
Fixed Radius ◽  
Python Package

scholarly journals BiSulfite Bolt: A bisulfite sequencing analysis platform

GigaScience ◽  
2021 ◽  
Vol 10 (5) ◽  
Author(s):  
Colin Farrell ◽  
Michael Thompson ◽  
Anela Tosevska ◽  
Adewale Oyetunde ◽  
Matteo Pellegrini
Keyword(s):  
Data Aggregation ◽  
Bisulfite Sequencing ◽  
Low Complexity ◽  
Sequencing Analysis ◽  
Command Line ◽  
Sequencing Data ◽  
Bisulfite Sequencing Data ◽  
Analysis Platform ◽  
Python Package ◽  
Bisulfite Sequencing Analysis

Abstract Background Bisulfite sequencing is commonly used to measure DNA methylation. Processing bisulfite sequencing data is often challenging owing to the computational demands of mapping a low-complexity, asymmetrical library and the lack of a unified processing toolset to produce an analysis-ready methylation matrix from read alignments. To address these shortcomings, we have developed BiSulfite Bolt (BSBolt), a fast and scalable bisulfite sequencing analysis platform. BSBolt performs a pre-alignment sequencing read assessment step to improve efficiency when handling asymmetrical bisulfite sequencing libraries. Findings We evaluated BSBolt against simulated and real bisulfite sequencing libraries. We found that BSBolt provides accurate and fast bisulfite sequencing alignments and methylation calls. We also compared BSBolt to several existing bisulfite alignment tools and found BSBolt outperforms Bismark, BSSeeker2, BISCUIT, and BWA-Meth based on alignment accuracy and methylation calling accuracy. Conclusion BSBolt offers streamlined processing of bisulfite sequencing data through an integrated toolset that offers support for simulation, alignment, methylation calling, and data aggregation. BSBolt is implemented as a Python package and command line utility for flexibility when building informatics pipelines. BSBolt is available at https://github.com/NuttyLogic/BSBolt under an MIT license.

scholarly journals SynBiopython: an open-source software library for Synthetic Biology

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Jing Wui Yeoh ◽  
Neil Swainston ◽  
Peter Vegh ◽  
Valentin Zulkower ◽  
Pablo Carbonell ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Open Source ◽  
Open Source Software ◽  
Development Projects ◽  
Software Library ◽  
Current State ◽  
Starting Point ◽  
Common Problems ◽  
Data Tracking ◽  
Python Package

Abstract Advances in hardware automation in synthetic biology laboratories are not yet fully matched by those of their software counterparts. Such automated laboratories, now commonly called biofoundries, require software solutions that would help with many specialized tasks such as batch DNA design, sample and data tracking, and data analysis, among others. Typically, many of the challenges facing biofoundries are shared, yet there is frequent wheel-reinvention where many labs develop similar software solutions in parallel. In this article, we present the first attempt at creating a standardized, open-source Python package. A number of tools will be integrated and developed that we envisage will become the obvious starting point for software development projects within biofoundries globally. Specifically, we describe the current state of available software, present usage scenarios and case studies for common problems, and finally describe plans for future development. SynBiopython is publicly available at the following address: http://synbiopython.org.

scholarly journals TAILOR-MS, a Python Package that Deciphers Complex Triacylglycerol Fatty Acyl Structures: Applications for Bovine Milk and Infant Formulas

2021 ◽  
Author(s):  
Kang-Yu Peng ◽  
Malinda Salim ◽  
Joseph Pelle ◽  
Gisela Ramirez ◽  
Ben J. Boyd
Keyword(s):  
Bovine Milk ◽  
Fatty Acyl ◽  
Infant Formulas ◽  
Python Package
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