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Open source tools and toolkits for bioinformatics: significance, and where are we?

J. E. Stajich
2006 Briefings in Bioinformatics  
Rather than creating a comprehensive list of all tools developed over the last 2^3 years, we use a few selected projects encompassing toolkit libraries, analysis tools, data analysis environments and interoperability  ...  standards to show how freely available and modifiable open-source software can serve as the foundation for building important applications, analysis workflows and resources.  ...  Many of these tools and toolkits are open source, allowing them to be folded into other applications and pipelines as reusable building blocks.  ... 
doi:10.1093/bib/bbl026 pmid:16899494 fatcat:x2dugkcc2vdv7j3b4ry6jkpiba

Efforts Towards Accessible And Reliable Bioinformatics

Matúš Kalaš, Inge Jonassen
2015 Zenodo  
As diverse components are necessary for the accessible and reliable bioinformatics scenario, our work focussed in particular on the following: In the BioXSD project, we aimed at developing an XML-Schema-based  ...  EDAM can be helpful in documenting and categorising bioinformatics resources using a standard "vocabulary", enabling users to find respective resources and choose the right tools.  ...  Many bioinformatics tools and toolkits are implemented as an open-source core library, with other interfaces -such as command-line, GUI, or web app -built on top of it.  ... 
doi:10.5281/zenodo.33715 fatcat:2pxqpqu5yvat3ctdedqam3sjsi

BioWarehouse: a bioinformatics database warehouse toolkit

Thomas J Lee, Yannick Pouliot, Valerie Wagner, Priyanka Gupta, David W J Stringer-Calvert, Jessica D Tenenbaum, Peter D Karp
2006 BMC Bioinformatics  
We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers.  ...  BioWarehouse embodies significant progress on the database integration problem for bioinformatics.  ...  We extend our thanks to Eric Sparling, Rich Giuli, John Pedersen, and Mark Johnson for their assistance in the design and development of the BioWarehouse.  ... 
doi:10.1186/1471-2105-7-170 pmid:16556315 pmcid:PMC1444936 fatcat:il65m27cyrhs7kunpci2ktifiq

Virtual reality in bioinformatics

Pritee Chunarkar Patil, Tanisha Batra
2019 Open Access Journal of Science  
In this paper we study about the different applications of Virtual Reality in Bioinformatics and also the history of Virtual reality.  ...  We take a brief look towards the immersive analytics of virtual reality. The tools used to produce the virtual environment are also being acknowledged with incorporating this knowledge.  ...  Shaikh, Principal, Rajiv Gandhi Institute of IT and Biotechnology, for kind blessing and encouragement.  ... 
doi:10.15406/oajs.2019.03.00132 fatcat:sxxbkx7xrbew3cg6adtlma34zy

Aptamer Bioinformatics

Lewis Fraser, Shaolin Liang, Simon Shiu, Julian Tanner
2017 International Journal of Molecular Sciences  
As aptamers are genetic in nature, bioinformatic approaches have been used to improve both aptamers and their selection.  ...  They are isolated via SELEX (Systematic Evolution of Ligands by Exponential Enrichment), an evolutionary process that involves iterative rounds of selection and amplification before sequencing and aptamer  ...  However, multiple open-source/paid bioinformatics tools have been developed specifically for aptamer scientists.  ... 
doi:10.3390/ijms18122516 pmid:29186809 pmcid:PMC5751119 fatcat:2uz7lb4lmjcsze5purtxjvhrci

Crowdfunding genomics and bioinformatics

Pamela Cameron, David W Corne, Christopher E Mason, Jeffrey Rosenfeld
2013 Genome Biology  
In addition, it will be web-based, easy to use, free and open source.  ...  Toolkit (LMAT), We anticipate that our project will result in an innovative method for city-level pathogen monitoring.  ... 
doi:10.1186/gb-2013-14-9-134 pmid:24079746 pmcid:PMC4054678 fatcat:hx6iopfarngzdezjj4uykrp7gi

Exploring the Toolkits of Predictive Analytics Practitioners-Part2

Richard Boire
2016 MOJ Proteomics & Bioinformatics  
We are still in the early stages of open-source products as an option in building data science solutions.  ...  The growing demand for predictive analytics/data science practitioners has resulted in the increase of open-source products that are readily available and virtually free to anyone with a computer and appetite  ... 
doi:10.15406/mojpb.2016.04.00116 fatcat:mk6jh73vqnc7pkr4z6bunnkvgq

Bioinformatics for precision oncology

Jochen Singer, Anja Irmisch, Hans-Joachim Ruscheweyh, Franziska Singer, Nora C Toussaint, Mitchell P Levesque, Daniel J Stekhoven, Niko Beerenwinkel
2017 Briefings in Bioinformatics  
To deliver on this promise of precision oncology, appropriate bioinformatics methods for managing, integrating and analyzing large and complex data are necessary.  ...  Here, we discuss the specific requirements of bioinformatics methods and software that arise in the setting of clinical oncology, owing to a stricter regulatory environment and the need for rapid, highly  ...  Another source of artifacts are sequencing adapters. Adapters are short nucleotide sequences attached to the genomic DNA fragment and used for amplification and sequencing.  ... 
doi:10.1093/bib/bbx143 pmid:29272324 fatcat:dkmf2usssnbgvltxbqepquk24u

Comprehensive data infrastructure for plant bioinformatics

Chris Jordan, Dan Stanzione, Doreen Ware, Jerry Lu, Christos Noutsos
2010 2010 IEEE International Conference On Cluster Computing Workshops and Posters (CLUSTER WORKSHOPS)  
Handling the large quantities of data involved in high-throughput sequencing and other experimental sources of bioinformatics data requires a robust infrastructure for storing and reusing large data objects  ...  and we describe the data model that has been developed to express and exchange data within the Discovery Environment, along with the provenance model defined for capturing experimental source and digital  ...  ACKNOWLEDGMENT The authors would like to thank the National Science Foundation for supporting the iPlant Collaborative.  ... 
doi:10.1109/clusterwksp.2010.5613093 fatcat:u6vwfeqeg5c5pobrsnasnw3uae

Experimenting with reproducibility in bioinformatics [article]

Yang-Min Kim, Jean-Baptiste Poline, Guillaume Dumas
2017 bioRxiv   pre-print
Here, we present a case study of our attempt to reproduce a promising bioinformatics method [1] and illustrate the challenges to use a published method for which code and data were available.  ...  First, we tried to re-run the analysis with the code and data provided by the au-thors.  ...  la Recherche Scientifique; University Paris Diderot; the Conny-Maeva Charitable Foundation; the Cognacq-Jay Foundation; the Orange Foundation; Fondation pour la Recherche Médicale; the GenMed Labex; and  ... 
doi:10.1101/143503 fatcat:m5zmfdhcorgytcptl3sgo3i7qy

Web and Grid Technologies in Bioinformatics, Computational and Systems Biology: A Review

Natalio Krasnogor, Azhar Shah, Daniel Barthel, Piotr Lukasiak, Jacek Blazewicz
2008 Current Bioinformatics  
In this paper we present a trace of these technological changes in Web and Grid technology, including details of emerging infrastructures, standards, languages and tools, as they apply to bioinformatics  ...  / Open source controlled-vocabularies for different biomedical domains GO [28] Gene Ontology http://www.geneontology.org/ Controlled-vocabulary for genes GMOD [55] Generic Model Organism Database http:  ...  environment for grid-enabled bioinformatics application using a set of open source tools  ... 
doi:10.2174/157489308783329850 fatcat:thpj6eywwvg5tfdqvbw5nch3ty

Atlas - a data warehouse for integrative bioinformatics

Sohrab P Shah, Yong Huang, Tao Xu, Macaire M S Yuen, John Ling, B F Francis Ouellette
2005 BMC Bioinformatics  
The Atlas system is based on relational data models that we developed for each of the source data types.  ...  We present use cases that use Atlas to integrate these sources for genome annotation, inference of molecular interactions across species, and gene-disease associations.  ...  Acknowledgements TX is supported by CIHR grant #MOP-53259, Juergen Kast and BFFO. We thank Miroslav Hatas and Graeme Campbell for systems administration support. We thank Michael E.  ... 
doi:10.1186/1471-2105-6-34 pmid:15723693 pmcid:PMC554782 fatcat:pfhx5xq65jhtlnl5ldl2kblvbq

Buying in to bioinformatics: an introduction to commercial sequence analysis software

David Roy Smith
2014 Briefings in Bioinformatics  
designed for non-computer specialists and marketed as one-stop bioinformatics toolkits.  ...  Although several commercial bioinformatics programs are arguably overpriced and overhyped, many are well designed, sophisticated and, in my opinion, worth the investment.  ...  ' of open-source tools, which makes them easy to modify and develop.  ... 
doi:10.1093/bib/bbu030 pmid:25183247 pmcid:PMC4501248 fatcat:w7sl6cr5vndknhu6xvrkczxdlu

Bioinformatics applied to gene transcription regulation

Gioia Altobelli
2012 Journal of Molecular Endocrinology  
It provides an outlook on tools and methods, selected from a host of bioinformatics resources available today.  ...  Diverse bioinformatics tools have been developed to help unravel these mechanisms, by handling and processing data at different stages: from data collection and storage to the identification of molecular  ...  R Flower, and Mr J Maftin for kindly proofreading the manuscript.  ... 
doi:10.1530/jme-12-0060 pmid:22723668 fatcat:tmxaon25zjfw5bbfqw7i56nih4

Building cyberinfrastructure for bioinformatics using service oriented architecture

W.W. Li, S. Krishnan, K. Mueller, K. Ichikawa, S. Date, S. Dallakyan, M. Sanner, C. Misleh, Zhaohui Ding, Xiaohui Wei, O. Tatebe, P.W. Arzberger
2006 Sixth IEEE International Symposium on Cluster Computing and the Grid (CCGRID'06)  
Here we describe an end to end prototype environment that allows existing applications to run on the grid, taking advantage of open source software that provides a portal interface using GridSphere, with  ...  Cyberinfrastructure makes the development and deployment of bioinformatics applications easier by providing the framework and components that may be loosely coupled using service oriented architecture.  ...  Packaging and deployment of custom actors for other users is still an open issue, and efforts are currently underway to handle the same. B.  ... 
doi:10.1109/ccgrid.2006.1630932 fatcat:bszkz5mfqzapbkl52mkynojxny
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