A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Filters
Open source tools and toolkits for bioinformatics: significance, and where are we?
2006
Briefings in Bioinformatics
Preserved Fulltext
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
2015
Zenodo
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
2006
BMC Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2019
Open Access Journal of Science
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2017
International Journal of Molecular Sciences
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
2013
Genome Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2014; you can also visit the original URL.
The file type is application/pdf.
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
2016
MOJ Proteomics & Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
2017
Briefings in Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2010
2010 IEEE International Conference On Cluster Computing Workshops and Posters (CLUSTER WORKSHOPS)
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2015; you can also visit the original URL.
The file type is application/pdf.
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]
2017
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2008
Current Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2005
BMC Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2014
Briefings in Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2012
Journal of Molecular Endocrinology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2006
Sixth IEEE International Symposium on Cluster Computing and the Grid (CCGRID'06)
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
« Previous
Showing results 1 — 15 out of 5,360 results