scholarly journals BIOFFORC: Tool development for biological file format conversion

2008 ◽  
Vol 3 (2) ◽  
pp. 98-99
Author(s):  
Chinnaiah Swaminathan Vinobha ◽  
Maruthamuthu Rajadurai ◽  
Ekambaram Rajasekaran
2019 ◽  
Author(s):  
Andrew Webb ◽  
Jared Knoblauch ◽  
Nitesh Sabankar ◽  
Apeksha Sukesh Kallur ◽  
Jody Hey ◽  
...  

AbstractHere we present the Pop-Gen Pipeline Platform (PPP), a software platform with the goal of reducing the computational expertise required for conducting population genomic analyses. The PPP was designed as a collection of scripts that facilitate common population genomic workflows in a consistent and standardized Python environment. Functions were developed to encompass entire workflows, including: input preparation, file format conversion, various population genomic analyses, output generation, and visualization. By facilitating entire workflows, the PPP offers several benefits to prospective end users - it reduces the need of redundant in-house software and scripts that would require development time and may be error-prone, or incorrect. The platform has also been developed with reproducibility and extensibility of analyses in mind. The PPP is an open-source package that is available for download and use at https://ppp.readthedocs.io/en/latest/PPP_pages/install.html


Applied laser ◽  
2014 ◽  
Vol 34 (4) ◽  
pp. 366-370
Author(s):  
罗曼 Luo Man ◽  
潘涌 Pan Yong ◽  
张瑄珺 Zhang Xuanjun ◽  
李浩 Li Hao ◽  
安博言 An Boyan

Applied laser ◽  
2014 ◽  
Vol 34 (4) ◽  
pp. 366-370
Author(s):  
罗曼 Luo Man ◽  
潘涌 Pan Yong ◽  
张瑄珺 Zhang Xuanjun ◽  
李浩 Li Hao ◽  
安博言 An Boyan

GigaScience ◽  
2021 ◽  
Vol 10 (2) ◽  
Author(s):  
Petr Danecek ◽  
James K Bonfield ◽  
Jennifer Liddle ◽  
John Marshall ◽  
Valeriu Ohan ◽  
...  

Abstract Background SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. Findings The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. Conclusion Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed >1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org.


2019 ◽  
Author(s):  
Natalie Wagner ◽  
Anita Acai ◽  
Sydney A. McQueen ◽  
Com McCarthy ◽  
Andrew McGuire ◽  
...  

Objective: The purpose of this study was to develop, implement, and evaluate the effectiveness of an assessment framework aimed at improving formative feedback practices in a Canadian orthopaedic postgraduate training program. Methods: Tool development began in 2014 and took place in 4 phases, each building upon the previous and informing the next. The reliability, validity, and educational impact of the tools were assessed on an ongoing basis, and changes were made accordingly. Results: One hundred eighty-two tools were completed and analyzed during the study period. Quantitative results suggested moderate to excellent agreement between raters (intraclass correlation coefficient = 0.54-0.93), and an ability of the tools to discriminate between learners at different stages of training (p’s < 0.05). Qualitative data suggested that the tools improved both the quality and quantity of formative feedback given by assessors and had begun to foster a culture change around assessment in the program. Conclusions: The tool development, implementation, and evaluation processes detailed in this article can serve as a model for other training programs to consider as they move towards adopting competency-based approaches and refining current assessment practices.


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