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Bioinformatics tools developed to support BioCompute Objects

Janisha A Patel, Dennis A Dean, Charles Hadley King, Nan Xiao, Soner Koc, Ekaterina Minina, Anton Golikov, Phillip Brooks, Robel Kahsay, Rahi Navelkar, Manisha Ray, Dave Roberson (+3 others)
2021 Database: The Journal of Biological Databases and Curation  
BioCompute Objects (BCOs) provide the requisite support for communication of HTS data analysis that includes support for workflow, as well as data, curation, accessibility and reproducibility of communication  ...  Developments in high-throughput sequencing (HTS) result in an exponential increase in the amount of data generated by sequencing experiments, an increase in the complexity of bioinformatics analysis reporting  ...  Funding This project was supported in part by funds from the NIH National Cancer Institute (awards HHSN261201400008C and HHSN261201500003I for Cancer Genomics Cloud and for development of the CGC BCO App  ... 
doi:10.1093/database/baab008 pmid:33784373 fatcat:32edkjmnonbjnhmid5lcf3prre

BCO App: tools for generating BioCompute Objects from next-generation sequencing workflows and computations

Nan Xiao, Soner Koc, David Roberson, Phillip Brooks, Manisha Ray, Dennis Dean
2020 F1000Research  
We created the BCO App to facilitate BCO generation in a range of computational environments and, in part, to participate in the Advanced Track of the precisionFDA BioCompute Object App-a-thon.  ...  The BioCompute Object (BCO) standard is an IEEE standard (IEEE 2791-2020) designed to facilitate the communication of next-generation sequencing data analysis with applications across academia, government  ...  Acknowledgments We appreciate the support from the Mazumder Lab at George Washington University in deploying the BCO App as part of an extra credit assignment for a first-year graduate bioinformatics course  ... 
doi:10.12688/f1000research.25902.1 pmid:33299553 pmcid:PMC7702177 fatcat:qh4lt3ricvhkzmqhijdxtfb774

Enabling Precision Medicine via standard communication of NGS provenance, analysis, and results [article]

Gil Alterovitz, Dennis A Dean, Carole Goble, Michael R Crusoe, Stian Soiland-Reyes, Amanda Bell, Anais Hayes, Anita Suresh, Charles Hadley S King, Dan Taylor, KanakaDurga Addepalli, Elaine Johanson (+23 others)
2017 bioRxiv   pre-print
The BioCompute paradigm and the resulting BioCompute Objects (BCOs) offer that umbrella.  ...  Thus, a resulting bioinformatics computation instance that includes these advancements can be easily communicated, repeated and compared by scientists, regulators, test developers and clinicians.  ...  In order to form a more cooperative community we have migrated all of the BioCompute development to GitHub (https://github.com/biocompute-objects), and are following the "Open-Stand.org principles for  ... 
doi:10.1101/191783 fatcat:6idjm4omhzasfofouk22akgdqy

Enabling precision medicine via standard communication of HTS provenance, analysis, and results

Gil Alterovitz, Dennis Dean, Carole Goble, Michael R. Crusoe, Stian Soiland-Reyes, Amanda Bell, Anais Hayes, Anita Suresh, Anjan Purkayastha, Charles H. King, Dan Taylor, Elaine Johanson (+25 others)
2018 PLoS Biology  
Bioinformatics computation instances that employ the BioCompute framework are easily relayed, repeated if needed, and compared by scientists, regulators, test developers, and clinicians.  ...  The BioCompute paradigm and the resulting BioCompute Objects (BCOs) offer that standard and are freely accessible as a GitHub organization (https://github.com/biocompute-objects) following the "Open-Stand.org  ...  Acknowledgments We would like to recognize all the speakers and participants of the 2017 HTS-CSRS workshop who facilitated the discussion on standardizing HTS computations and analyses.  ... 
doi:10.1371/journal.pbio.3000099 pmid:30596645 pmcid:PMC6338479 fatcat:dh5fphvtazd5xlzu3vtl6cata4

Biocompute Objects—A Step towards Evaluation and Validation of Biomedical Scientific Computations

Vahan Simonyan, Jeremy Goecks, Raja Mazumder
2016 PDA journal of pharmaceutical science and technology  
In this article we describe the concept of biocompute objects developed specifically to satisfy regulatory research needs for evaluation, validation, and verification of bioinformatics pipelines.  ...  We envision generalized versions of biocompute objects called biocompute templates that support a single class of analyses but can be adapted to meet unique needs.  ...  Acknowledgments We would like to mention with gratitude the following people for providing valuable comments regarding research and regulatory aspects to HTS:  ... 
doi:10.5731/pdajpst.2016.006734 pmid:27974626 pmcid:PMC5510742 fatcat:bmuqdqok4fevxecpwoekw47euq

Biocompute 2.0: an improved collaborative workspace for data intensive bio-science

Rory Carmichael, Patrick Braga-Henebry, Douglas Thain, Scott Emrich
2011 Concurrency and Computation  
If tool developers need only specify the interface for the initial execution of their tool, it greatly simplifies the addition of new actions to the system.  ...  In this paper, we describe the goals and interface to the system, its architecture and performance, and the insights gained in its development. Biocompute is arranged into three primary components.  ...  ACKNOWLEDGEMENTS We would like to acknowledge the hard work of Joey Rich, Ryan Jansen, Thomas Potthaus, and Brian Kachmark who greatly assisted in the implementation of Biocompute.  ... 
doi:10.1002/cpe.1782 fatcat:fzcwy6kg7bcjvmoshbnk45vzlm

Development of software tools at BioInformatics Centre (BIC) at the National University of Singapore (NUS)

P R Kolatkar, M K Sakharkar, C R Tse, B K Kiong, L Wong, T W Tan, S Subbiah
1998 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
The recently formed BioInformatics Centre (BIC) at the National University of Singapore (NUS) provides access to various commonly used computational tools available over the World Wide Web (WWW)--using  ...  For this the life sciences today needs tools in information technology and computation to prevent degeneration of this data into an inchoate accretion of unconnected facts and figures.  ...  Acknowledgment Bioinformatics Centre (NUS), is funded by the Economic Development Board (EDB) of Singapore. Subbiah .S acknowledges DOE grant no. DE-FG03-95ER62135 for partial support.  ... 
pmid:9697226 fatcat:dwqftnm73rbsrpzzzoswiscqtu

Biocompute

Rory Carmichael, Patrick Braga-Henebry, Douglas Thain, Scott Emrich
2010 Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing - HPDC '10  
The resulting web portal, Biocompute, has been in production use at the University of Notre Dame's Bioinformatics Core Facility since the summer of 2009.  ...  The explosion of data in the biological community demands the development of more scalable and flexible portals for bioinformatic computation.  ...  A tool developer need not be intimately familiar with biocompute in order to develop a module.  ... 
doi:10.1145/1851476.1851547 dblp:conf/hpdc/CarmichaelBTE10 fatcat:lctvsrrk5zfq7a2ub3yiprynai

GOBLET - The Global Organisation for Bioinformatics Learning, Education & Training

Celia W.G. Van Gelder, Domenica D'Elia, Eija Korpelainen
2021 Zenodo  
SocArXiv, 3, doi:10.31235/osf.io/7qeht Mastery Rubric for Bioinformatics (MR-Bi) • Tool to support curriculum design & evaluation  ...  mygoblet.org GOBLET Objectives • Set standards and provide high-quality resources to support learning, education and training • Provide a Training Portal to become both a pull mechanism and repository  ... 
doi:10.5281/zenodo.5131570 fatcat:6cdkb6k73zfthfnlvm2gogaiku

Machine learning and deep analytics for biocomputing: call for better explainability

Dragutin Petkovic, Lester Kobzik, Christopher Re
2017 Biocomputing 2018  
and practical guidance to the biocomputing community on how to address these challenges and how to develop improvements.  ...  as in the development of new costly medical procedures and drugs.  ...  Specifically, we believe that improved explainability of MLDA in biocomputing will result in the following benefits: increased credibility and confidence in its application; improved ability to objectively  ... 
doi:10.1142/9789813235533_0058 fatcat:mlrr32f5ofb57k7b2brht3xgqq

Utility library for structural bioinformatics

D. Gront, A. Kolinski
2008 Bioinformatics  
In this Note we present a new software library for structural bioinformatics.  ...  Finally, the new version of BioShell delivers several utility programs that can do typical bioinformatics task from a command-line level.  ...  Scripting with BioShell is intended to be the main way to access its modules. finally the jbcl (Java BioComputing Library) that holds over 80% of BioShell code can be directly used to develop JAVA programs  ... 
doi:10.1093/bioinformatics/btm627 pmid:18227118 fatcat:rx2s4ipxpzelng3iptay2o4coy

APPLICATIONS OF GENETICS, GENOMICS AND BIOINFORMATICS IN DRUG DISCOVERY

RICHARD BOURGON, FREDERICK E. DEWEY, ZHENGYAN KAN, SHUYU D. LI
2017 Biocomputing 2018  
As the impact of genetics, genomics, and bioinformatics on drug discovery has been increasingly recognized, this session of the 2018 Pacific Symposium on Biocomputing (PSB) aims to facilitate scientific  ...  The selected papers focus on developing and applying computational approaches to understand drug mechanisms of action and develop drug combination strategies, to enable in silico drug screening, and to  ...  Acknowledgments We thank our respective organizations for supporting our involvement in organizing the session.  ... 
doi:10.1142/9789813235533_0001 fatcat:cg5lcjpmejbpfpslhjzgyfhrke

A review of Bioinformatics training applied to research in Molecular Medicine, Agriculture and Biodiversity in Costa Rica and Central America

A. Orozco, J. Morera, S. Jimenez, R. Boza
2013 Briefings in Bioinformatics  
The recent creation of the Central American Bioinformatics Network (BioCANET), associated to the deployment of a supporting computational infrastructure (HPC Cluster) devoted to provide computing support  ...  , leading to the creation of the region's first Bioinformatics Master's Degree.  ...  and biocomputing tools.  ... 
doi:10.1093/bib/bbt033 pmid:23723382 fatcat:dq5xqnstabdlplsp2h7jckarfa

The Bioinformatics Template Library--generic components for biocomputing

W. R. Pitt, M. A. Williams, M. Steven, B. Sweeney, A. J. Bleasby, D. S. Moss
2001 Bioinformatics  
allows them to be flexibly combined with application specific object-oriented class libraries.  ...  This library will facilitate the rapid development of efficient programs by providing efficient code for many algorithms and data-structures that are commonly used in biocomputing, in a generic form that  ...  This work was supported by a BBSRC/EPSRC grant BIF05348 within the Bioinformatics Programme.  ... 
doi:10.1093/bioinformatics/17.8.729 pmid:11524374 fatcat:6d4yqyy74rctjlblugagwmylmu

The Machine that Builds Itself: How the Strengths of Lisp Family Languages Facilitate Building Complex and Flexible Bioinformatic Models [article]

Bohdan B. Khomtchouk, Edmund Weitz, Claes Wahlestedt
2016 arXiv   pre-print
We are convinced that Lisp grants programmers unprecedented power to build increasingly sophisticated artificial intelligence systems that may ultimately transform machine learning and AI research in bioinformatics  ...  We will also show how these features make these languages ideal tools for artificial intelligence and machine learning applications.  ...  Symbolic biocomputing has also previously been used to create user-friendly visual tools for interactive data analysis and exploration [49] .  ... 
arXiv:1608.02621v2 fatcat:ykuxzohhxbcbtlzxrvgwaa2ame
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