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The Gaggle: an open-source software system for integrating bioinformatics software and data sources

Paul T Shannon, David J Reiss, Richard Bonneau, Nitin S Baliga
2006 BMC Bioinformatics  
In this paper we describe the Gaggle -a simple, open-source Java software environment that helps to solve the problem of software and database integration.  ...  Systems biologists work with many kinds of data, from many different sources, using a variety of software tools.  ...  Acknowledgements We thank Nat Goodman and Burak Kutlu for critical reading of the manuscript and helpful suggestions.  ... 
doi:10.1186/1471-2105-7-176 pmid:16569235 pmcid:PMC1464137 fatcat:wcucwxamejb3tdzpmdywlimjle

Enabling high-throughput data management for systems biology: The Bioinformatics Resource Manager

A. R. Shah, M. Singhal, K. R. Klicker, E. G. Stephan, H. S. Wiley, K. M. Waters
2007 Bioinformatics  
The Bioinformatics Resource Manager (BRM) is a software environment that provides the user with data management, retrieval and integration capabilities.  ...  BRM is developed using Java TM and other open-source technologies for free distribution.  ...  ACKNOWLEDGEMENTS The research described in this article was conducted under the LDRD Program at the Pacific Northwest National Laboratory, a multiprogram national laboratory operated by Battelle for the  ... 
doi:10.1093/bioinformatics/btm031 pmid:17324940 fatcat:6zcslqw2avgy3ag26dnqus7gji

Integration and visualization of systems biology data in context of the genome

J Christopher Bare, Tie Koide, David J Reiss, Dan Tenenbaum, Nitin S Baliga
2010 BMC Bioinformatics  
The program handles large sets of usergenerated data using an in-process database and leverages the facilities of SQL and the R environment for importing and manipulating data.  ...  Important features include dynamic panning and zooming, keyword search and open interoperability through the Gaggle framework.  ...  Acknowledgements This work was supported by grants from NSF (DBI-0640950), NIH (1R01GM077398 and P50GM076547), DOE (MAGGIE: DE-FG02-07ER64327) and Battelle (214610) to NSB.  ... 
doi:10.1186/1471-2105-11-382 pmid:20642854 pmcid:PMC2912892 fatcat:myezg3bnsfbwhkjayhtmgwxqja

R-Based Software for the Integration of Pathway Data into Bioinformatic Algorithms

Frank Kramer, Michaela Bayerlová, Tim Beißbarth
2014 Biology  
In this review, we examine software packages for the statistical computing framework R, which enable the integration of pathway data for further bioinformatic analyses.  ...  Furthermore, prior knowledge can increase the performance and stability of bioinformatic algorithms, for example, methods for network reconstruction.  ...  This manuscript aims to give an overview of software packages for the R Project for Statistical Computing that integrate pathway data for bioinformatic analysis within R.  ... 
doi:10.3390/biology3010085 pmid:24833336 pmcid:PMC4009765 fatcat:op62z6xt7jgwnkmdbabf4veaiq

The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications

J Christopher Bare, Paul T Shannon, Amy K Schmid, Nitin S Baliga
2007 BMC Bioinformatics  
But integrating data from multiple sources is often encumbered by the need to reformat data files, convert between naming systems, or perform ongoing maintenance of local copies of public databases.  ...  Opportunities for new ways of combining and re-using data are arising as a result of the increasing use of web protocols to transmit structured data.  ...  Acknowledgements We thank Dan Tenenbaum and Ricardo Vencio for critical reading of the manuscript and helpful suggestions.  ... 
doi:10.1186/1471-2105-8-456 pmid:18021453 pmcid:PMC2211326 fatcat:cxjycpe7g5gozczab5qno32tka

Prequips--an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data

N. Gehlenborg, W. Yan, I. Y. Lee, H. Yoo, K. Nieselt, D. Hwang, R. Aebersold, L. Hood
2009 Bioinformatics  
We describe an integrative software platform, Prequips, for comparative proteomicsbased systems biology analysis that: (i) integrates all information generated from mass spectrometry (MS)-based proteomics  ...  as well as from basic proteomics data analysis tools, (ii) visualizes such information for various proteomic analyses via graphical interfaces and (iii) links peptide and protein abundances to external  ...  Data providers, designed in plug-in interfaces, separate Prequips Prequips-an extensible software platform from the data sources (e.g. mzXML, pepXML and protXML; Fig. 1A ) and make the software independent  ... 
doi:10.1093/bioinformatics/btp005 pmid:19129212 pmcid:PMC2720692 fatcat:cf6rmnia3zfu3c34z7lrbzqbie

Data management strategies for multinational large-scale systems biology projects

W. Wruck, M. Peuker, C. R. A. Regenbrecht
2012 Briefings in Bioinformatics  
Here, we give an overview of a selection of open-source data management systems proved to be employed successfully in large-scale projects.  ...  Good accessibility of publicly funded research data is essential to secure an open scientific system and eventually becomes mandatory [ Wellcome Trust will Penalise Scientists Who Don't Embrace Open Access  ...  The authors acknowledge support from the German Federal Ministry of Education and Research (BMBF GRANT 0315717A), which is a partner of the ERASysBioþ initiative supported under the EU ERA-NET Plus scheme  ... 
doi:10.1093/bib/bbs064 pmid:23047157 pmcid:PMC3896927 fatcat:ivmmnprxzzg4tckczjkthgdeoi

Architecture for interoperable software in biology

J. C. Bare, N. S. Baliga
2012 Briefings in Bioinformatics  
We provide a few guidelines for the development of future software that will function as part of an interoperable community of software tools for biological data analysis and visualization.  ...  One way to bring to bear the necessary combination of data types and expertise is by encapsulating domain knowledge in software and composing that software to create a customized data analysis environment  ...  We also thank the reviewers for their helpful comments and suggestions.  ... 
doi:10.1093/bib/bbs074 pmid:23235920 pmcid:PMC4103535 fatcat:2glzz3ah4jbafkbfelnjxwdupq

Bioinformatics resource manager v2.3: an integrated software environment for systems biology with microRNA and cross-species analysis tools

Susan C Tilton, Tamara L Tal, Sheena M Scroggins, Jill A Franzosa, Elena S Peterson, Robert L Tanguay, Katrina M Waters
2012 BMC Bioinformatics  
The Bioinformatics Resource Manager (BRM) v2.3 is a software environment for data management, mining, integration and functional annotation of HTP biological data.  ...  The miRNA workflow in BRM allows for efficient processing of multiple miRNA and mRNA datasets in a single software environment with the added capability to interact with public data sources and visual  ...  Berst's summer fellowship in the Tanguay laboratory. We also thank Tara Gibson for implementation of the software updates and Hao Truong for the custom behavior analysis script.  ... 
doi:10.1186/1471-2105-13-311 pmid:23174015 pmcid:PMC3534564 fatcat:mjjd3ntwsvbhdi3edjaeypqcym

The Artificial Intelligence Workbench: a retrospective review

2016 Advances in Distributed Computing and Artificial Intelligence Journal  
In this context, the Artificial Intelligence Workbench, an open-source Java desktop application framework for scientific software development, emerged with the goal of providing support to both fundamental  ...  and applied research in the domain of translational biomedicine and bioinformatics.  ...  Acknowledgements The authors would like to thank all the valuable comments, ideas and discussion from the high number of AIBench developers who have contributed towards the improvement of our framework  ... 
doi:10.14201/adcaij2016517385 fatcat:cmz5ruhxijeydipsfrstzai4ni

Bioclipse: an open source workbench for chemo- and bioinformatics

Ola Spjuth, Tobias Helmus, Egon L Willighagen, Stefan Kuhn, Martin Eklund, Johannes Wagener, Peter Murray-Rust, Christoph Steinbeck, Jarl ES Wikberg
2007 BMC Bioinformatics  
The rich functionality, intuitive user interface, and powerful plugin architecture make Bioclipse the most advanced and user-friendly open source workbench for chemo-and bioinformatics.  ...  There is a need for software applications that provide users with a complete and extensible toolkit for chemo-and bioinformatics accessible from a single workbench.  ...  Acknowledgements The authors thank Mark Southern for adapting the SequenceViewer to the Bioinformatics Perspective and Jerome Pansanel for generating sample chemical structures.  ... 
doi:10.1186/1471-2105-8-59 pmid:17316423 pmcid:PMC1808478 fatcat:qm5wuudbz5ho7cw5n4j7fjlaam

Software Tool for Researching Annotations of Proteins: Open-Source Protein Annotation Software with Data Visualization

Vivek N. Bhatia, David H. Perlman, Catherine E. Costello, Mark E. McComb
2009 Analytical Chemistry  
Here we present the Software Tool for Researching Annotations of Proteins (STRAP), a userfriendly, open-source C# application.  ...  lists may be encoded in the Gaggle microformat for further characterization, including pathway analysis.  ...  ACKNOWLEDGMENT We thank all the members of the Center for Biomedical Mass Spectrometry for evaluating STRAP and providing feedback during the course of program development.  ... 
doi:10.1021/ac901335x pmid:19839595 pmcid:PMC2787672 fatcat:dlkhbongo5b67gvvmcoyux47yq

BioNetBuilder: automatic integration of biological networks

I. Avila-Campillo, K. Drew, J. Lin, D. J. Reiss, R. Bonneau
2006 Bioinformatics  
BioNetBuilder is an open-source client-server Cytoscape plugin that offers a user-friendly interface to create biological networks integrated from several databases.  ...  Users can create networks for 1500 organisms, including common model organisms and human. Currently supported databases include: DIP, BIND, Prolinks, KEGG, HPRD, The BioGrid and GO, among others.  ...  ACKNOWLEDGEMENTS We would like to thank Lee Hood, Peter Bowers and Junghwan Park. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btl604 pmid:17138585 fatcat:hwnkiqilo5hsvh5ee3swwm5nuq

An Analysis of Scripting Languages for Research in Applied Computing

Olugbenga Oluwagbemi, Adewole Adewumi, Sanjay Misra, Folakemi Majekodunmi, Luis Fernandez
2013 2013 IEEE 16th International Conference on Computational Science and Engineering  
Accordingly, based on selected criteria we determine their suitability in the fields of software engineering, bioinformatics and computational biology research.  ...  Particularly in applied computing fields like software engineering, bioinformatics and computational biology, scripting languages are gaining popularity.  ...  It first appeared in 1990 and is an open-source product of more than twenty years of cutting-edge research which allows rapid development of robust, concise, correct software.  ... 
doi:10.1109/cse.2013.174 dblp:conf/cse/OluwagbemiAMMS13 fatcat:sj7jtg3hyjeg5hmhl7n37ep244

Open Source Drug Discovery with Bioclipse

Ola Spjuth, Lars Carlsson, Jonathan Alvarsson, Valentin Georgiev, Egon Willighagen, Martin Eklund
2012 Current Topics in Medicinal Chemistry  
We present the open source components for drug discovery that has been developed and integrated into the graphical workbench Bioclipse.  ...  Bioclipse is used in both academia and industry, and is a good example of open source leading to new solutions for drug discovery.  ...  Acknowledgements The authors would like to acknowledge the Bioclipse developers and the OpenTox Project, especially Roman Affentrager who developed the original Malaria use case for Bioclipse Decision  ... 
doi:10.2174/156802612804910287 pmid:23110533 fatcat:4icucxbyfzgt7b5wc2pgh7aaxu
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