scholarly journals Measuring the Shape and Size of Activated Sludge Particles Immobilized in Agar with an Open Source Software Pipeline

10.3791/58963 ◽  
2019 ◽  
Author(s):  
Joseph E. Weaver ◽  
Jon C. Williams ◽  
Joel J. Ducoste ◽  
Francis L. de los Reyes
Keyword(s):  
Activated Sludge ◽  
Open Source ◽  
Open Source Software ◽  
Software Pipeline ◽  
Shape And Size

scholarly journals The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples

2019 ◽  
Author(s):  
H. Soon Gweon ◽  
Liam P. Shaw ◽  
Jeremy Swann ◽  
Nicola De Maio ◽  
Manal AbuOun ◽  
...  
Keyword(s):  
Data Processing ◽  
Open Source ◽  
Open Source Software ◽  
River Sediment ◽  
Taxonomic Composition ◽  
Sequencing Depth ◽  
Gene Content ◽  
Metagenomic Data ◽  
Software Pipeline ◽  
Shotgun Metagenomics

ABSTRACTBackgroundShotgun metagenomics is increasingly used to characterise microbial communities, particularly for the investigation of antimicrobial resistance (AMR) in different animal and environmental contexts. There are many different approaches for inferring the taxonomic composition and AMR gene content of complex community samples from shotgun metagenomic data, but there has been little work establishing the optimum sequencing depth, data processing and analysis methods for these samples. In this study we used shotgun metagenomics and sequencing of cultured isolates from the same samples to address these issues. We sampled three potential environmental AMR gene reservoirs (pig caeca, river sediment, effluent) and sequenced samples with shotgun metagenomics at high depth (∼200 million reads per sample). Alongside this, we cultured single-colony isolates ofEnterobacteriaceaefrom the same samples and used hybrid sequencing (short- and long-reads) to create high-quality assemblies for comparison to the metagenomic data. To automate data processing, we developed an open-source software pipeline, ‘ResPipe’.ResultsTaxonomic profiling was much more stable to sequencing depth than AMR gene content. 1 million reads per sample was sufficient to achieve <1% dissimilarity to the full taxonomic composition. However, at least 80 million reads per sample were required to recover the full richness of different AMR gene families present in the sample, and additional allelic diversity of AMR genes was still being discovered in effluent at 200 million reads per sample. Normalising the number of reads mapping to AMR genes using gene length and an exogenous spike ofThermus thermophilusDNA substantially changed the estimated gene abundance distributions. While the majority of genomic content from cultured isolates from effluent was recoverable using shotgun metagenomics, this was not the case for pig caeca or river sediment.ConclusionsSequencing depth and profiling method can critically affect the profiling of polymicrobial animal and environmental samples with shotgun metagenomics. Both sequencing of cultured isolates and shotgun metagenomics can recover substantial diversity that is not identified using the other methods. Particular consideration is required when inferring AMR gene content or presence by mapping metagenomic reads to a database. ResPipe, the open-source software pipeline we have developed, is freely available (https://gitlab.com/hsgweon/ResPipe).

scholarly journals The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples

2019 ◽  
Vol 14 (1) ◽  
Author(s):  
H. Soon Gweon ◽  
◽  
Liam P. Shaw ◽  
Jeremy Swann ◽  
Nicola De Maio ◽  
...  
Keyword(s):  
Data Processing ◽  
Open Source ◽  
Open Source Software ◽  
River Sediment ◽  
Taxonomic Composition ◽  
Sequencing Depth ◽  
Gene Content ◽  
Metagenomic Data ◽  
Software Pipeline ◽  
Shotgun Metagenomics

Abstract Background Shotgun metagenomics is increasingly used to characterise microbial communities, particularly for the investigation of antimicrobial resistance (AMR) in different animal and environmental contexts. There are many different approaches for inferring the taxonomic composition and AMR gene content of complex community samples from shotgun metagenomic data, but there has been little work establishing the optimum sequencing depth, data processing and analysis methods for these samples. In this study we used shotgun metagenomics and sequencing of cultured isolates from the same samples to address these issues. We sampled three potential environmental AMR gene reservoirs (pig caeca, river sediment, effluent) and sequenced samples with shotgun metagenomics at high depth (~ 200 million reads per sample). Alongside this, we cultured single-colony isolates of Enterobacteriaceae from the same samples and used hybrid sequencing (short- and long-reads) to create high-quality assemblies for comparison to the metagenomic data. To automate data processing, we developed an open-source software pipeline, ‘ResPipe’. Results Taxonomic profiling was much more stable to sequencing depth than AMR gene content. 1 million reads per sample was sufficient to achieve < 1% dissimilarity to the full taxonomic composition. However, at least 80 million reads per sample were required to recover the full richness of different AMR gene families present in the sample, and additional allelic diversity of AMR genes was still being discovered in effluent at 200 million reads per sample. Normalising the number of reads mapping to AMR genes using gene length and an exogenous spike of Thermus thermophilus DNA substantially changed the estimated gene abundance distributions. While the majority of genomic content from cultured isolates from effluent was recoverable using shotgun metagenomics, this was not the case for pig caeca or river sediment. Conclusions Sequencing depth and profiling method can critically affect the profiling of polymicrobial animal and environmental samples with shotgun metagenomics. Both sequencing of cultured isolates and shotgun metagenomics can recover substantial diversity that is not identified using the other methods. Particular consideration is required when inferring AMR gene content or presence by mapping metagenomic reads to a database. ResPipe, the open-source software pipeline we have developed, is freely available (https://gitlab.com/hsgweon/ResPipe).

scholarly journals Towards an open-source pipeline for patient-specific neurosurgery simulation

2011 ◽  
Author(s):  
Andinet Enquobahrie ◽  
Michel Audette ◽  
Huai-ping Lee
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Significant Proportion ◽  
Patient Specific ◽  
Surgery Simulation ◽  
Software Pipeline ◽  
Simulation Based ◽  
Two Parameters ◽  
Surgery Simulator ◽  
Novice Surgeons

Surgery simulation is a technology based on interactive biomechanics as well as haptic and visual rendering for training novice surgeons. Another important component of a surgery simulator is the representation of a patient’s anatomy in terms of simple shapes, typically triangles and tetrahedra, coinciding with relevant tissues, whose manipulation, cutting and resection is simulated. While this technology has so far emphasized generic simulators, increasingly researchers are emphasizing models that derive from the images of patients whose pathology collectively are predictive of a significant proportion of the future caseload of surgeons. In addition, our philosophy of producing patient-specific neurosurgery simulators is to organize the architecture in terms of two parameters: the choice of approach- pterional, trans-nasal, frontal and so on, and the nature of the pathology, which in turn determines the specific nature of the treatment and choice of tools. This paper describes on-going work on the refinement of an open-source software pipeline for producing patient-specific neurosurgery simulation, based on segmentation tools such as those available in Slicer and BrainVisa, surface and volume meshing, such as public VTK-based tools and Tetgen respectively, and the SOFA simulation platform. Practical requirements of the various components of the pipeline, such as resolution control and fidelity of surface and volume meshing, and interactive nonlinear mechanics in the biomechanics engine, are discussed.

An Algorithm for Gradual Patch Acceptance Detection in Open Source Software Repository Mining

2012 ◽  
Vol E95.A (9) ◽  
pp. 1478-1489
Author(s):  
Passakorn PHANNACHITTA ◽  
Akinori IHARA ◽  
Pijak JIRAPIWONG ◽  
Masao OHIRA ◽  
Ken-ichi MATSUMOTO
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Software Repository ◽  
Repository Mining ◽  
Software Repository Mining

Hacking Diversity

2019 ◽  
Author(s):  
Christina Dunbar-Hester
Keyword(s):  
Open Source ◽  
Human Resource ◽  
Open Source Software ◽  
Cultural Production ◽  
Equal Opportunity ◽  
Economic Power ◽  
Underrepresented Groups ◽  
Technical Production ◽  
Preferred Solutions

Hacking, as a mode of technical and cultural production, is commonly celebrated for its extraordinary freedoms of creation and circulation. Yet surprisingly few women participate in it: rates of involvement by technologically skilled women are drastically lower in hacking communities than in industry and academia. This book investigates the activists engaged in free and open-source software to understand why, despite their efforts, they fail to achieve the diversity that their ideals support. The book shows that within this well-meaning volunteer world, beyond the sway of human resource departments and equal opportunity legislation, members of underrepresented groups face unique challenges. The book explores who participates in voluntaristic technology cultures, to what ends, and with what consequences. Digging deep into the fundamental assumptions underpinning STEM-oriented societies, the book demonstrates that while the preferred solutions of tech enthusiasts—their “hacks” of projects and cultures—can ameliorate some of the “bugs” within their own communities, these methods come up short for issues of unequal social and economic power. Distributing “diversity” in technical production is not equal to generating justice. The book reframes questions of diversity advocacy to consider what interventions might appropriately broaden inclusion and participation in the hacking world and beyond.

Web Based GIS Application using Open Source Software for Sharing Geospatial Data

2015 ◽  
Vol 4 (1) ◽  
pp. 1224-1228 ◽  
Author(s):  
Debasish Chakraborty ◽  
◽  
Debanjan Sarkar ◽  
Shubham Agarwal ◽  
Dibyendu Dutta ◽  
...  
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Geospatial Data ◽  
Web Based ◽  
Gis Application
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