scholarly journals The Popgen Pipeline Platform: A Software Platform for Facilitating Population Genomic Analyses

2019 ◽  
Author(s):  
Andrew Webb ◽  
Jared Knoblauch ◽  
Nitesh Sabankar ◽  
Apeksha Sukesh Kallur ◽  
Jody Hey ◽  
...  
Keyword(s):  
Open Source ◽  
Development Time ◽  
End Users ◽  
File Format ◽  
Software Platform ◽  
Format Conversion ◽  
Link Type ◽  
Population Genomic ◽  
Genomic Analyses ◽  
File Format Conversion

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

File Format Conversion and Optimization Techniques of Laser Show Multimedia Material

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
Keyword(s):  
Optimization Techniques ◽  
File Format ◽  
Format Conversion ◽  
Multimedia Material ◽  
File Format Conversion

scholarly journals Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs

2021 ◽  
Author(s):  
Soohyun Lee ◽  
Carl Vitzthum ◽  
Burak H. Alver ◽  
Peter J. Park
Keyword(s):  
Quality Control ◽  
Open Source ◽  
Source Code ◽  
Three Dimensional ◽  
File Format ◽  
Interaction Data ◽  
Text File ◽  
Storage And Retrieval ◽  
Link Type ◽  
Efficient Storage

AbstractSummaryAs the amount of three-dimensional chromosomal interaction data continues to increase, storing and accessing such data efficiently becomes paramount. We introduce Pairs, a block-compressed text file format for storing paired genomic coordinates from Hi-C data, and Pairix, an open-source C application to index and query Pairs files. Pairix (also available in Python and R) extends the functionalities of Tabix to paired coordinates data. We have also developed PairsQC, a collapsible HTML quality control report generator for Pairs files.AvailabilityThe format specification and source code are available at https://github.com/4dn-dcic/pairix, https://github.com/4dn-dcic/Rpairix and https://github.com/4dn-dcic/[email protected] or [email protected]

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
Keyword(s):  
Tool Development ◽  
File Format ◽  
Format Conversion ◽  
File Format Conversion

File Format Conversion and Optimization Techniques of Laser Show Multimedia Material

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
Keyword(s):  
Optimization Techniques ◽  
File Format ◽  
Format Conversion ◽  
Multimedia Material ◽  
File Format Conversion

scholarly journals PDBeCIF: an open-source mmCIF/CIF parsing and processing package

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Glen van Ginkel ◽  
Lukáš Pravda ◽  
José M. Dana ◽  
Mihaly Varadi ◽  
Peter Keller ◽  
...  
Keyword(s):  
Open Source ◽  
Protein Data Bank ◽  
Hybrid Methods ◽  
Structural Data ◽  
Data Bank ◽  
File Format ◽  
Macromolecular Complexes ◽  
Link Type ◽  
Information File ◽  
Multiscale Structures

Abstract Background Biomacromolecular structural data outgrew the legacy Protein Data Bank (PDB) format which the scientific community relied on for decades, yet the use of its successor PDBx/Macromolecular Crystallographic Information File format (PDBx/mmCIF) is still not widespread. Perhaps one of the reasons is the availability of easy to use tools that only support the legacy format, but also the inherent difficulties of processing mmCIF files correctly, given the number of edge cases that make efficient parsing problematic. Nevertheless, to fully exploit macromolecular structure data and their associated annotations such as multiscale structures from integrative/hybrid methods or large macromolecular complexes determined using traditional methods, it is necessary to fully adopt the new format as soon as possible. Results To this end, we developed PDBeCIF, an open-source Python project for manipulating mmCIF and CIF files. It is part of the official list of mmCIF parsers recorded by the wwPDB and is heavily employed in the processes of the Protein Data Bank in Europe. The package is freely available both from the PyPI repository (http://pypi.org/project/pdbecif) and from GitHub (https://github.com/pdbeurope/pdbecif) along with rich documentation and many ready-to-use examples. Conclusions PDBeCIF is an efficient and lightweight Python 2.6+/3+ package with no external dependencies. It can be readily integrated with 3rd party libraries as well as adopted for broad scientific analyses.

Pedigree and Pedigree Import Wizard

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 552g-553
Author(s):  
Shahrokh Khandizadeh
Keyword(s):  
Additional Data ◽  
File Format ◽  
Fruit Crops ◽  
Operating Environment ◽  
Agronomic Characteristics ◽  
Link Type ◽  
Plant Characteristics ◽  
User Friendly

Pedigree for Windows is a user-friendly program that allows the user to trace agronomic characteristics, draw pedigrees, and view images of several fruit crops, including more than 1400 apple, 800 strawberry, 800 almond, 100 blackberry, 80 blueberry, 790 pear, 200 raspberry examples. Pedigree Import Wizard®© for Windows is an add-on software for users who are interested in importing their research or breeding data records of fruit, flower, and plant characteristics and any related images into Pedigree for Windows. Pedigree for Windows and Pedigree Import Wizard have been designed so that a user familiar with the Windows operating environment should have little need to refer to the documentation provided with the program. Pedigree Import Wizard uses a comma-separated value (csv) file format under the MS Excel environment. This option allows the user to add or import additional data to the existing database that are already stored in other software such as Lotus, Excel, Access, QuattroPro, WordPerfect, and MS Word tables, etc., as long as they work under the Windows environment. A free demo version of Pedigree and Pedigree Import Wizard for Windows is available from http://www.pgris.com.

scholarly journals Integrated multi-modality image-guided navigation for neurosurgery: open-source software platform using state-of-the-art clinical hardware

2021 ◽  
Author(s):  
Jonathan Shapey ◽  
Thomas Dowrick ◽  
Rémi Delaunay ◽  
Eleanor C. Mackle ◽  
Stephen Thompson ◽  
...  
Keyword(s):  
Skull Base ◽  
Open Source ◽  
Open Source Software ◽  
Skull Base Surgery ◽  
Patient Specific ◽  
Software Platform ◽  
Image Guided ◽  
Phantom Model ◽  
Technical Requirements ◽  
Navigated Ultrasound

Abstract Purpose Image-guided surgery (IGS) is an integral part of modern neuro-oncology surgery. Navigated ultrasound provides the surgeon with reconstructed views of ultrasound data, but no commercial system presently permits its integration with other essential non-imaging-based intraoperative monitoring modalities such as intraoperative neuromonitoring. Such a system would be particularly useful in skull base neurosurgery. Methods We established functional and technical requirements of an integrated multi-modality IGS system tailored for skull base surgery with the ability to incorporate: (1) preoperative MRI data and associated 3D volume reconstructions, (2) real-time intraoperative neurophysiological data and (3) live reconstructed 3D ultrasound. We created an open-source software platform to integrate with readily available commercial hardware. We tested the accuracy of the system’s ultrasound navigation and reconstruction using a polyvinyl alcohol phantom model and simulated the use of the complete navigation system in a clinical operating room using a patient-specific phantom model. Results Experimental validation of the system’s navigated ultrasound component demonstrated accuracy of $$<4.5\,\hbox {mm}$$ < 4.5 mm and a frame rate of 25 frames per second. Clinical simulation confirmed that system assembly was straightforward, could be achieved in a clinically acceptable time of $$<15\,\hbox {min}$$ < 15 min and performed with a clinically acceptable level of accuracy. Conclusion We present an integrated open-source research platform for multi-modality IGS. The present prototype system was tailored for neurosurgery and met all minimum design requirements focused on skull base surgery. Future work aims to optimise the system further by addressing the remaining target requirements.

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