Papers by Katherine G Herbert
A mobile tool for collecting scientific experimental data
2015 IEEE Integrated STEM Education Conference, 2015
Authentication, Access Control, and Intrusion Detection
Computer Science Handbook, Second Edition CD-ROM, 2004
... and how security violations have occurred or been attempted. Auditing requires registration o... more ... and how security violations have occurred or been attempted. Auditing requires registration or ... trail, or audit log. The nature and format of this data varies from system to system. Information which should be recorded for each event includes the subject requesting the access, ...
GeoTagger
Proceedings of the companion publication of the 17th ACM conference on Computer supported cooperative work & social computing - CSCW Companion '14, 2014
ABSTRACT This note focuses on the motivation, approach, and the initial prototype implementation ... more ABSTRACT This note focuses on the motivation, approach, and the initial prototype implementation of Geotagger: a collaborative participatory environmental inquiry system. We situate the need for such a technology, and discuss related work -- much of which is situated in the realm of citizen science. Our work uniquely distinguishes itself from many other citizen science applications in that it supports limited data collection and analysis, with the additional benefit of supporting social interactions and engagement through conversations about observed data. This is accomplished by creating friends and groups which are collaborators in the observational inquiry process.
Ligand Variations in New Sulfonamide-Supported Group 4 Ring-Opening Polymerization Catalysts
Organometallics, 2010
... Paniagua and Philip Mountford*. ... The four-coordinate 25 was the most active, forming poly(... more ... Paniagua and Philip Mountford*. ... The four-coordinate 25 was the most active, forming poly(ε-CL) with a relatively narrow PDI and well-controlled M n . Compounds 22, 23, 25, and 26 and isopropoxides generated in situ from 30−32 were all active for the ROP of rac-lactide. ...
Synthesis of glycosylated 5-hydroxylysine, an important amino acid present in collagen-like proteins such as adiponectin
Organic & Biomolecular Chemistry, 2012
The synthesis of naturally occurring glycosylated (2S,5R)-hydroxylysine still remains a challenge... more The synthesis of naturally occurring glycosylated (2S,5R)-hydroxylysine still remains a challenge. This perspective highlights the importance of this post-translationally modified amino acid residue in the observed bioactivity of collagen and related collagen-like proteins such as adiponectin, an important target for the treatment of type II diabetes. Strategies employed to date for the syntheses of (2S,5R)-hydroxylysine and the methods to effect glycosylation of this modified amino acid are also summarized herein.
XML Query by Example
Ijcia, 2002
ABSTRACT XML's tree structure provides a rich background for complicated structural searc... more ABSTRACT XML's tree structure provides a rich background for complicated structural searches. In this paper we present a new system, called XML Query by Example (XML QBE) that allows the user to query XML documents exploiting their inherent tree structure. We present some interesting queries and describe the underlying query processing algorithms. We also describe the system's architecture and report its implementation status. Finally we conclude the paper by pointing out some future work.
Proceedings of the 17th International Conference on Scientific and Statistical Database Management, 2005
With the increase of genome and proteome data, phylogenetic information and phylogenetic analysis... more With the increase of genome and proteome data, phylogenetic information and phylogenetic analysis tools are increasing greatly in current biological repositories. First, many repositories allow users to browse information about species through taxonomic tools. These tools present the species with its lineage path and links to the various types of information the repository provides about the species. Second, some multiple sequence alignment tools offer users basic phylogenetic data through applying basic reconstruction algorithms to the alignment. With the availability of this information in multiple locations, integrated tools are needed to allow the user to compare this data. This paper presents data integration research on lineage paths using the BIO-AJAX framework. It introduces BIO-AJAX for Lineage Paths, a tool that integrates lineage path information for NCBI Taxonomy
Current Developments in Big Data and Sustainability Sciences in Mobile Citizen Science Applications
2015 IEEE First International Conference on Big Data Computing Service and Applications, 2015
Fecs, 2008
The choice of programming language, the approach by which students are taught and the software to... more The choice of programming language, the approach by which students are taught and the software tools made available to students have been controversial issues in many ways. While there once was a consensus of some sort within the computer science education community, it is much more difficult to find common ground among those of us who teach introductory programming courses. The literature is explored and answers sought to the question of which language is optimum in teaching novice programmers, as well as the approach that ought to be used. Finally, the question of whether a consensus can be reached is addressed.
Algorithms and Software for Calculating and Visualizing the Cardinality of the Grand Bounding Ball by Means of Intersection Trees
Int. Conf. on Data Mining, 2008
Geotagger: A collaborative environmental inquiry platform
2015 International Conference on Collaboration Technologies and Systems (CTS), 2015
Toward an Integrated RNA Motif Database
Lecture Notes in Computer Science, 2007
ABSTRACT In this paper we present the design and implementation of an RNA structural motif databa... more ABSTRACT In this paper we present the design and implementation of an RNA structural motif database, called RmotifDB. The structural motifs stored in RmotifDB come from three sources: (1) collected manually from biomedical literature; (2) submitted by scientists around the world; and (3) discovered by a wide variety of motif mining methods. We present here a motif mining method in detail. We also describe the interface and search mechanisms provided by RmotifDB as well as techniques used to integrate RmotifDB with the Gene Ontology. The RmotifDB system is fully operational and accessible on the Internet at http://datalab.njit.edu/bioinfo/
GeoTagger
Proceedings of the companion publication of the 17th ACM conference on Computer supported cooperative work & social computing - CSCW Companion '14, 2014
ABSTRACT This note focuses on the motivation, approach, and the initial prototype implementation ... more ABSTRACT This note focuses on the motivation, approach, and the initial prototype implementation of Geotagger: a collaborative participatory environmental inquiry system. We situate the need for such a technology, and discuss related work -- much of which is situated in the realm of citizen science. Our work uniquely distinguishes itself from many other citizen science applications in that it supports limited data collection and analysis, with the additional benefit of supporting social interactions and engagement through conversations about observed data. This is accomplished by creating friends and groups which are collaborators in the observational inquiry process.
An interdisciplinary undergraduate science informatics degree in a liberal arts context
ACM SIGCSE Bulletin, 2006
ABSTRACT In this paper, we describe a new interdisciplinary B.S. degree in Science Informatics at... more ABSTRACT In this paper, we describe a new interdisciplinary B.S. degree in Science Informatics at Montclair State University, a multipurpose public institution that includes a substantial General Education component. Beginning in the freshmen year, the Science Informatics curriculum contains 16 semester hours of interdisciplinary science informatics courses including a freshmen experience, internships, a research component, ethics, and a concentration currently in bioinformatics, cheminformatics, or computer science as well as core science and mathematics courses.
A study of phylogenetic tools for genomic nomenclature data cleaning
ACM SIGCSE Bulletin, 2007
ABSTRACT In this poster we propose a method for addressing the genomic nomenclature problem by us... more ABSTRACT In this poster we propose a method for addressing the genomic nomenclature problem by using phylogenetic tools along with the BIO-AJAX data cleaning framework.
A New Kernel Method for RNA Classification
Sixth IEEE Symposium on BioInformatics and BioEngineering (BIBE'06), 2006
Support vector machines (SVMs) are a state-of-the-art machine learning tool widely used in speech... more Support vector machines (SVMs) are a state-of-the-art machine learning tool widely used in speech recognition, image processing and biological sequence analysis. An essential step in SVMs is to devise a kernel function to compute the similarity between two data points in Euclidean space. In this paper we present a new kernel that takes advantage of both global and local structural information in RNAs and uses the information together to classify RNAs with support vector machines. Experimental results demonstrate the good performance of the new kernel and show that it outperforms existing kernels when applied to classifying non-coding RNA sequences
Prediction of modulators of pyruvate kinase in smiles text using aprori methods
ACM SIGCSE Bulletin, 2007
ABSTRACT Pyruvate kinase is an enzyme that catalyzes the formation of pyruvate from phosphenolpyr... more ABSTRACT Pyruvate kinase is an enzyme that catalyzes the formation of pyruvate from phosphenolpyruvate in glycolysis. There is a wealth of data on the activity of certain molecules and their effects on pyruvate kinase. This project aims to create an application that uses a pyruvate kinase dataset to determine the nature of unidentified molecules; whether or not they would be activators or inhibitors of this enzyme. This application uses an Apriori algorithm to identify or predict modulators of pyruvate kinase. This initial study focuses on simplified molecular input line entry specification (SMILES) text as target data to be mined. The three dimensional structure of pyruvate kinase is known and accessible though the Protein Data Bank (e.g., PDB code IA3W).
Integrating interdisciplinary science into high school science modules through a preproinsulin example
ACM SIGMOD Record, 2004
As databases become more pervasive through the biological sciences, various
Bioinformatic Databases
Wiley Encyclopedia of Computer Science and Engineering, 2007
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Papers by Katherine G Herbert