Ronald Nowling - Academia.edu (original) (raw)

Papers by Ronald Nowling

This poster presents the release of the CONNJUR Spectrum Translator: an open source software tool... more This poster presents the release of the CONNJUR Spectrum Translator: an open source software tool which converts time-domain NMR data between Varian, Bruker, nmrPipe and RNMRTK formats. It is envisioned that the open source nature of CONNJUR will facilitate the addition of other available file formats.

2014 IEEE Fourth International Conference on Big Data and Cloud Computing, 2014

2011 Eighth International Conference on Information Technology: New Generations, 2011

ABSTRACT Encoding for solutions of combinatorial optimization problems involving permutations or ... more ABSTRACT Encoding for solutions of combinatorial optimization problems involving permutations or constraints that maintain the generality of operators in evolutionary computation is often difficult. In this paper, we present the Priority Encoding Scheme (PES), a general-purpose encoding scheme that encodes information used to construct solutions rather than directly encoding solutions themselves. We show that not only is PES simple to implement, but that it can be used effectively with Genetic Algorithms (GA) and Simulated Annealing (SA) to find good solutions to the multiple-constraint knapsack problem (MKP) and shows promise for finding good solutions to the traveling salesman problem (TSP).

2011 Eighth International Conference on Information Technology: New Generations, 2011

The CONNecticut Joint University Research (CONNJUR) team is a group of biochemical and software e... more The CONNecticut Joint University Research (CONNJUR) team is a group of biochemical and software engineering researchers at multiple institutions. The vision of the team is to develop a comprehensive application that integrates a variety of existing analysis tools with workflow and data management to support the process of protein structure determination using Nuclear Magnetic Resonance (NMR). The use of multiple disparate tools and lack of data management, currently the norm in NMR data processing, provides strong motivation for such an integrated environment. This manuscript briefly describes the domain of NMR as used for protein structure determination and explains the formation of the CONNJUR team and its operation in developing the CONNJUR application. The manuscript also describes the evolution of the CONNJUR application through four prototypes and describes the challenges faced while developing the CONNJUR application and how those challenges were met.

Journal of Chemical Theory and Computation, 2013

Molecular dynamics (MD) simulations now play a key role in many areas of theoretical chemistry, b... more Molecular dynamics (MD) simulations now play a key role in many areas of theoretical chemistry, biology, physics, and materials science. In many cases, such calculations are significantly limited by the massive amount of computer time needed to perform calculations of interest. Herein, we present Long Timestep Molecular Dynamics (LTMD), a method to significantly speed MD simulations. In particular, we discuss new methods to calculate the needed terms in LTMD as well as issues germane to a GPU implementation. The resulting code, implemented in the OpenMM MD library, can achieve a significant 6-fold speed increase, leading to MD simulations on the order of 5 µs/day using implicit solvent models.

Journal of Biomolecular NMR, 2011

NMR spectroscopists are hindered by the lack of standardization for spectral data among the file ... more NMR spectroscopists are hindered by the lack of standardization for spectral data among the file formats for various NMR data processing tools. This lack of standardization is cumbersome as researchers must perform their own file conversion in order to switch between processing tools and also restricts the combination of tools employed if no conversion option is available. The CONNJUR Spectrum Translator introduces a new, extensible architecture for spectrum translation and introduces two key algorithmic improvements. This first is translation of NMR spectral data (time and frequency domain) to a single in-memory data model to allow addition of new file formats with two converter modules, a reader and a writer, instead of writing a separate converter to each existing format. Secondly, the use of layout descriptors allows a single fid data translation engine to be used for all formats. For the end user, sophisticated metadata readers allow conversion of the majority of files with minimum user configuration. The open source code is freely available at http://connjur.sourceforge.net for inspection and extension.

Computing in Science & Engineering, 2000

The problem of formatting data so that it conforms to the required input for scientific data proc... more The problem of formatting data so that it conforms to the required input for scientific data processing tools pervades scientific computing. The CONNecticut Joint University Research Group (CONNJUR) has developed a data translation tool based on a pipeline architecture that partially solves this problem. The CONNJUR Spectrum Translator supports data format translation for experiments that use Nuclear Magnetic Resonance to determine the structure of large protein molecules.

BMC Genomics, 2009

Background: One of the most important developments in bioinformatics over the past few decades ha... more Background: One of the most important developments in bioinformatics over the past few decades has been the observation that short linear peptide sequences (minimotifs) mediate many classes of cellular functions such as protein-protein interactions, molecular trafficking and posttranslational modifications. As both the creators and curators of a database which catalogues minimotifs, Minimotif Miner, the authors have a unique perspective on the commonalities of the many functional roles of minimotifs. There is an obvious usefulness in standardizing functional annotations both in allowing for the facile exchange of data between various bioinformatics resources, as well as the internal clustering of sets of related data elements. With these two purposes in mind, the authors provide a proposed syntax for minimotif semantics primarily useful for functional annotation.

BMC Bioinformatics, 2010

Background: Minimotifs are short peptide sequences within one protein, which are recognized by ot... more Background: Minimotifs are short peptide sequences within one protein, which are recognized by other proteins or molecules. While there are now several minimotif databases, they are incomplete. There are reports of many minimotifs in the primary literature, which have yet to be annotated, while entirely novel minimotifs continue to be published on a weekly basis. Our recently proposed function and sequence syntax for minimotifs enables us to build a general tool that will facilitate structured annotation and management of minimotif data from the biomedical literature.

Parasites & Vectors, 2013

Background: The control of vector-borne diseases, such as malaria, dengue fever, and typhus fever... more Background: The control of vector-borne diseases, such as malaria, dengue fever, and typhus fever is often achieved with the use of insecticides. Unfortunately, insecticide resistance is becoming common among different vector species. There are currently no chemical alternatives to these insecticides because new human-safe classes of molecules have yet to be brought to the vector-control market. The identification of novel targets offer opportunities for rational design of new chemistries to control vector populations. One target family, G proteincoupled receptors (GPCRs), has remained relatively under explored in terms of insecticide development. Methods: A novel classifier, Ensemble*, for vector GPCRs was developed. Ensemble* was validated and compared to existing classifiers using a set of all known GPCRs from Aedes aegypti, Anopheles gambiae, Apis Mellifera, Drosophila melanogaster, Homo sapiens, and Pediculus humanus. Predictions for unidentified sequences from Ae. aegypti, An. gambiae, and Pe. humanus were validated. Quantitative RT-PCR expression analysis was performed on previously-known and newly discovered Ae. aegypti GPCR genes.

This poster presents the release of the CONNJUR Spectrum Translator: an open source software tool... more This poster presents the release of the CONNJUR Spectrum Translator: an open source software tool which converts time-domain NMR data between Varian, Bruker, nmrPipe and RNMRTK formats. It is envisioned that the open source nature of CONNJUR will facilitate the addition of other available file formats.

2014 IEEE Fourth International Conference on Big Data and Cloud Computing, 2014

2011 Eighth International Conference on Information Technology: New Generations, 2011

ABSTRACT Encoding for solutions of combinatorial optimization problems involving permutations or ... more ABSTRACT Encoding for solutions of combinatorial optimization problems involving permutations or constraints that maintain the generality of operators in evolutionary computation is often difficult. In this paper, we present the Priority Encoding Scheme (PES), a general-purpose encoding scheme that encodes information used to construct solutions rather than directly encoding solutions themselves. We show that not only is PES simple to implement, but that it can be used effectively with Genetic Algorithms (GA) and Simulated Annealing (SA) to find good solutions to the multiple-constraint knapsack problem (MKP) and shows promise for finding good solutions to the traveling salesman problem (TSP).

2011 Eighth International Conference on Information Technology: New Generations, 2011

The CONNecticut Joint University Research (CONNJUR) team is a group of biochemical and software e... more The CONNecticut Joint University Research (CONNJUR) team is a group of biochemical and software engineering researchers at multiple institutions. The vision of the team is to develop a comprehensive application that integrates a variety of existing analysis tools with workflow and data management to support the process of protein structure determination using Nuclear Magnetic Resonance (NMR). The use of multiple disparate tools and lack of data management, currently the norm in NMR data processing, provides strong motivation for such an integrated environment. This manuscript briefly describes the domain of NMR as used for protein structure determination and explains the formation of the CONNJUR team and its operation in developing the CONNJUR application. The manuscript also describes the evolution of the CONNJUR application through four prototypes and describes the challenges faced while developing the CONNJUR application and how those challenges were met.

Journal of Chemical Theory and Computation, 2013

Molecular dynamics (MD) simulations now play a key role in many areas of theoretical chemistry, b... more Molecular dynamics (MD) simulations now play a key role in many areas of theoretical chemistry, biology, physics, and materials science. In many cases, such calculations are significantly limited by the massive amount of computer time needed to perform calculations of interest. Herein, we present Long Timestep Molecular Dynamics (LTMD), a method to significantly speed MD simulations. In particular, we discuss new methods to calculate the needed terms in LTMD as well as issues germane to a GPU implementation. The resulting code, implemented in the OpenMM MD library, can achieve a significant 6-fold speed increase, leading to MD simulations on the order of 5 µs/day using implicit solvent models.

Journal of Biomolecular NMR, 2011

NMR spectroscopists are hindered by the lack of standardization for spectral data among the file ... more NMR spectroscopists are hindered by the lack of standardization for spectral data among the file formats for various NMR data processing tools. This lack of standardization is cumbersome as researchers must perform their own file conversion in order to switch between processing tools and also restricts the combination of tools employed if no conversion option is available. The CONNJUR Spectrum Translator introduces a new, extensible architecture for spectrum translation and introduces two key algorithmic improvements. This first is translation of NMR spectral data (time and frequency domain) to a single in-memory data model to allow addition of new file formats with two converter modules, a reader and a writer, instead of writing a separate converter to each existing format. Secondly, the use of layout descriptors allows a single fid data translation engine to be used for all formats. For the end user, sophisticated metadata readers allow conversion of the majority of files with minimum user configuration. The open source code is freely available at http://connjur.sourceforge.net for inspection and extension.

Computing in Science & Engineering, 2000

The problem of formatting data so that it conforms to the required input for scientific data proc... more The problem of formatting data so that it conforms to the required input for scientific data processing tools pervades scientific computing. The CONNecticut Joint University Research Group (CONNJUR) has developed a data translation tool based on a pipeline architecture that partially solves this problem. The CONNJUR Spectrum Translator supports data format translation for experiments that use Nuclear Magnetic Resonance to determine the structure of large protein molecules.

BMC Genomics, 2009

Background: One of the most important developments in bioinformatics over the past few decades ha... more Background: One of the most important developments in bioinformatics over the past few decades has been the observation that short linear peptide sequences (minimotifs) mediate many classes of cellular functions such as protein-protein interactions, molecular trafficking and posttranslational modifications. As both the creators and curators of a database which catalogues minimotifs, Minimotif Miner, the authors have a unique perspective on the commonalities of the many functional roles of minimotifs. There is an obvious usefulness in standardizing functional annotations both in allowing for the facile exchange of data between various bioinformatics resources, as well as the internal clustering of sets of related data elements. With these two purposes in mind, the authors provide a proposed syntax for minimotif semantics primarily useful for functional annotation.

BMC Bioinformatics, 2010

Background: Minimotifs are short peptide sequences within one protein, which are recognized by ot... more Background: Minimotifs are short peptide sequences within one protein, which are recognized by other proteins or molecules. While there are now several minimotif databases, they are incomplete. There are reports of many minimotifs in the primary literature, which have yet to be annotated, while entirely novel minimotifs continue to be published on a weekly basis. Our recently proposed function and sequence syntax for minimotifs enables us to build a general tool that will facilitate structured annotation and management of minimotif data from the biomedical literature.

Parasites & Vectors, 2013

Background: The control of vector-borne diseases, such as malaria, dengue fever, and typhus fever... more Background: The control of vector-borne diseases, such as malaria, dengue fever, and typhus fever is often achieved with the use of insecticides. Unfortunately, insecticide resistance is becoming common among different vector species. There are currently no chemical alternatives to these insecticides because new human-safe classes of molecules have yet to be brought to the vector-control market. The identification of novel targets offer opportunities for rational design of new chemistries to control vector populations. One target family, G proteincoupled receptors (GPCRs), has remained relatively under explored in terms of insecticide development. Methods: A novel classifier, Ensemble*, for vector GPCRs was developed. Ensemble* was validated and compared to existing classifiers using a set of all known GPCRs from Aedes aegypti, Anopheles gambiae, Apis Mellifera, Drosophila melanogaster, Homo sapiens, and Pediculus humanus. Predictions for unidentified sequences from Ae. aegypti, An. gambiae, and Pe. humanus were validated. Quantitative RT-PCR expression analysis was performed on previously-known and newly discovered Ae. aegypti GPCR genes.