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Mark LeBlanc

Wheaton College, MA, Computer Science, Faculty Member

Wheaton College, MA, Mathematics and Computer Science, Faculty Member

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Dr. Mark D. LeBlanc is Professor of Computer Science at Wheaton College and Co-Director of the NEH-funded Lexomics Research Group. LeBlanc's early research in genomics, searching genomes of DNA for patterns, prepared him for this last decade of interdisciplinary research, specifically, building web-based tools for scholars who seek to explore their digitized texts. LeBlanc is actively involved in interdisciplinary teaching on Wheaton's campus, sharing computing across the academy. He presently co-directs Wheaton's new minor in the Digital Humanities (DH) and teaches a number of interdisciplinary courses, including "DNA" and "Computing for Poets", introductory programming courses for students in the life sciences and DH.

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Graduate Center of the City University of New York

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National and Kapodistrian University of Athens

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Papers by Mark LeBlanc

DNA and 普通話 (Mandarin): Bringing introductory programming to the Life Sciences and Digital Humanities

Procedia Computer Science, 2015

The ability to write software (to script, to program, to code) is a vital skill for students and ... more The ability to write software (to script, to program, to code) is a vital skill for students and their future data-centric, multidisciplinary careers. We present a ten-year effort to teach introductory programming skills in domain-focused courses to students across divisions in our liberal arts college. By creatively working with colleagues in Biology, Statistics, and now English, we have designed, modified, and offered six iterations of two courses: "DNA" and "Computing for Poets". Larger percentages of women have consistently enrolled in these two courses vs. the traditional first course in the major. We share our open source course materials and present here our use of a blended learning classroom that leverages the increasing quality of online video lectures and programming practice sites in an attempt to maximize faculty-student interactions in class.

10. Kathleen Davis, Periodization and Sovereignty: How Ideas of Feudalism and Secularization Govern the Politics of Time Kathleen Davis, Periodization and Sovereignty: How Ideas of Feudalism and Secularization Govern the Politics of Time (pp. 405-407)

Index for 2011

Lexos 2017: building reliable software in python

Journal of Computing Sciences in Colleges, 2018

Refactoring software is challenging, but necessary to ensure software correctness and extensibili... more Refactoring software is challenging, but necessary to ensure software correctness and extensibility. We present a plan that blends automated tools and human reviews when refactoring the back-end of a web-based application. The Lexos software, developed by the NEH-funded Lexomics Project, provides a simple, web-based workflow for text processing, statistical analysis, and visualization of results when exploring digitized texts. The development of Lexos spans six years and includes over fifty undergraduate developers, many who assumed leadership roles in architectural design and systems engineering over three software releases. This paper shares our current refactoring effort on the Python backend to produce Lexos v3.2, an effort that includes a transition from Python v2.7 to Python v3.6. Good software engineering practices guide the effort, including the use of type hinting, a Model-View-Control pattern, PEP 8 code and PEP 257 documentation styles, unit testing, and continuous integr...

Lexos: An Integrated Lexomics Workflow

Digital Humanities Conference, 2017

Lexos is a browser-based suite of tools that helps lower barriers of entry to computational text ... more Lexos is a browser-based suite of tools that helps lower barriers of entry to computational text analysis for humanities scholars and students. Situated within a clean and simple interface, Lexos consolidates the common pre-processing operations needed for subsequent analysis, either with Lexos or with external tools. It is especially useful for scholars who wish to engage in research involving computational text analysis and/or wish to teach their students how to do so but lack the time for a manual preparation of texts, the skill sets needed to prepare their texts analysis, or the intellectual contexts for situating computational methods within their work. Lexos is also targeted at researchers studying early texts and texts in non-Western languages, which may involve specialized processing rules. It is thus designed to facilitate advanced research in these fields even for users more familiar with computational techniques. Lexos is developed by the Lexomics research group led by Michael Drout

Essay Bioinformatics and the Undergraduate Curriculum Essay

Recent advances involving high-throughput techniques for data generation and analysis have made f... more Recent advances involving high-throughput techniques for data generation and analysis have made familiarity with basic bioinformatics concepts and programs a necessity in the biological sciences. Undergraduate students increasingly need training in methods related to finding and retrieving information stored in vast databases. The rapid rise of bioinformatics as a new discipline has challenged many colleges and universities to keep current with their curricula, often in the face of static or dwindling resources. On the plus side, many bioinformatics modules and related databases and software programs are free and accessible online, and interdisciplinary partnerships between existing faculty members and their sup-port staff have proved advantageous in such efforts. We present examples of strategies and methods that have been successfully used to incorporate bioinformatics content into under-graduate curricula.

Introducing Students to Explorations of Digitized Texts Using Lexos

String Play with Regular Expressions

Perl for Exploring DNA, 2007

Meeting Report: Incorporating Genomics Research into Undergraduate Curricula

Cell Biology Education, 2002

In the first of two National Science Foundation (NSF)funded workshops, 30 professors of biology a... more In the first of two National Science Foundation (NSF)funded workshops, 30 professors of biology and computer science from 18 institutions met at Wheaton College in Norton, Massachusetts, on June 6-7, 2002, to share ideas on how to incorporate genomics research into undergraduate curricula. The participants included nine pairs or trios of biologists and computer scientists, anticipating or already implementing collaborations. In a before-and-after format, the two workshops are intended to encourage experimentation in the classroom (June 2002) followed by reflection on and evaluation of ideas (June 2003). Interdisciplinary work is the heart of any research in genomics. The magnitude of the data sets and the scale of the problems require the expertise of individuals from both computer science and biology or biochemistry . Collaborations in the sciences are common in many research settings but can be difficult to implement in undergraduate classrooms, especially in a relatively new field such as genomics. Biology students need opportunities to ask original questions and participate in algorithm and software design to learn how to set up new projects with programmers. Likewise, programmers entering the field of genomics must have a richer facility with the types of analyses and hypotheses that are useful, and programmers could benefit from interactions with biologists who will be using their programs. Our goals and objectives for this initial workshop targeted these needs and are listed in Table . Following is a discussion of the six main outcomes of the June 2002 workshop. From our perspective, one of the more significant outcomes of the first workshop was the overwhelming number of participants who left feeling more confident about their ideas and feeling justified that new teaching models are needed. The

Bioinformatics and the Undergraduate Curriculum

Cell Biology Education, 2010

Recent advances involving high-throughput techniques for data generation and analysis have made f... more Recent advances involving high-throughput techniques for data generation and analysis have made familiarity with basic bioinformatics concepts and programs a necessity in the biological sciences. Undergraduate students increasingly need training in methods related to finding and retrieving information stored in vast databases. The rapid rise of bioinformatics as a new discipline has challenged many colleges and universities to keep current with their curricula, often in the face of static or dwindling resources. On the plus side, many bioinformatics modules and related databases and software programs are free and accessible online, and interdisciplinary partnerships between existing faculty members and their support staff have proved advantageous in such efforts. We present examples of strategies and methods that have been successfully used to incorporate bioinformatics content into undergraduate curricula.

Classification and regression tree (CART) analyses of genomic signatures reveal sets of tetramers that discriminate temperature optima of archaea and bacteria

Archaea, 2008

Classification and regression tree (CART) analysis was applied to genome-wide tetranucleotide fre... more Classification and regression tree (CART) analysis was applied to genome-wide tetranucleotide frequencies (genomic signatures) of 195 archaea and bacteria. Although genomic signatures have typically been used to classify evolutionary divergence, in this study, convergent evolution was the focus. Temperature optima for most of the organisms examined could be distinguished by CART analyses of tetranucleotide frequencies. This suggests that pervasive (nonlinear) qualities of genomes may reflect certain environmental conditions (such as temperature) in which those genomes evolved. The predominant use of GAGA and AGGA as the discriminating tetramers in CART models suggests that purine-loading and codon biases of thermophiles may explain some of the results.

Of Dendrogrammatology: Lexomic Methods for Analyzing Relationships among Old English Poems

The Journal of English and …, 2011

The genome of every organism is composed of millions of small chemical units called nucleobases, ... more

Pattern Recognition through Computational Stylistics: Old English and Beyond

Lexomics: Integrating the research and teaching spaces

Teaching together: a three-year case study in genomics

Journal of Computing Sciences in Colleges, 2003

The emerging field of "Genomics" (the analysis of DNA sequences) requires interdiscipli... more The emerging field of "Genomics" (the analysis of DNA sequences) requires interdisciplinary collaborations between computer scientists and biologists. Whereas most colleges and universities do not and may not ever have full programs in bioinformatics/genomics, new models of teaching and associated supporting materials are needed if we are to provide undergraduate science majors with experiences in the art of cooperation necessary to solve tomorrow's problems in genomics. We report here on our recent three-year experiences with "linking" computer science and biology courses. By infusing genomics into existing computer science and biology courses ("Algorithms," "Software Engineering," "Genetics," and "Cell Evolution"), interdisciplinary classes and labs in genomics are provided to all computer science majors and over half of all majors in the biological sciences (biology, biochemistry, environmental science, and psychobio...

Doing Their Own Math: Computer Support of Discursive Approaches to "Real" Math Problems

Traditionally, there has been no obvious role for the computer in an elementarylevel classroom or... more Traditionally, there has been no obvious role for the computer in an elementarylevel classroom oriented toward "talking about math" as a way of deepening children's understanding of mathematical problem situations. We suggest that an appropriate computer learning environment can serve as a useful tool to both complement and be enhanced by discursive approaches to mathematics. In this paper we describe software, some of which is currently being tested in classrooms, which allows students to create and share word problems motivated by classroom discussion of an arithmetically relevant situation, and to dynamically explore links between linguistic and other symbolic representations of their problems and those of other children. In conjunction with the discursive approach, these facilities support pedagogical methods such as the integration of writing, science and mathematics; roles for students as knowledge contributors rather than as passive recipients; and a motivated u...

Toward Reproducibility in DH Experiments: A Case Study in Search of Edgar Allan Poe's First Published Work

Reproducing experimental results is a hallmark of empirical investigation and serves both to veri... more Reproducing experimental results is a hallmark of empirical investigation and serves both to verify and inspire. This paper is a call for more systematic documentation of computational stylistic experiments. Publishing only summaries of the methods and results of empirical work is an artifact of traditional print media. To facilitate experimental reproducibility and to help the growing community who wish to learn how to apply computational methods and subsequently teach the next generation of scholars, the publication of results must include (i) access to the digitized texts, (ii) a clear workflow and most essentially (iii) the source code that led to each and all of the experimental results. By way of example, we present the steps and process in a GitHub repository for computationally probing the unknown and contested authorship of an 1831 short story entitled “A Dream” as we seek evidence if this work is similar to other attributed works by Edgar Allan Poe. The entire framework is...

Lexos: An Integrated Lexomics Workflow

Lexos is a browser-based suite of tools that helps lower barriers of entry to computational text ... more Lexos is a browser-based suite of tools that helps lower barriers of entry to computational text analysis for humanities scholars and students. Situated within a clean and simple interface, Lexos consolidates the common pre-processing operations needed for subsequent analysis, either with Lexos or with external tools. It is especially useful for scholars who wish to engage in research involving computational text analysis and/or wish to teach their students how to do so but lack the time for a manual preparation of texts, the skill sets needed to prepare their texts analysis, or the intellectual contexts for situating computational methods within their work. Lexos is also targeted at researchers studying early texts and texts in non-Western languages, which may involve specialized processing rules. It is thus designed to facilitate advanced research in these fields even for users more familiar with computational techniques. Lexos is developed by the Lexomics research group led by Mi...

A DNA motif lexicon: cataloguing and annotating sequences

In Silico Biology, 2004

ABSTRACT: The rapid proliferation of genomic DNA sequences has created a significant need for sof... more

EngageCSEduMaking interdisciplinary connections to engage students

ACM Inroads

DNA and 普通話 (Mandarin): Bringing introductory programming to the Life Sciences and Digital Humanities

Procedia Computer Science, 2015

The ability to write software (to script, to program, to code) is a vital skill for students and ... more The ability to write software (to script, to program, to code) is a vital skill for students and their future data-centric, multidisciplinary careers. We present a ten-year effort to teach introductory programming skills in domain-focused courses to students across divisions in our liberal arts college. By creatively working with colleagues in Biology, Statistics, and now English, we have designed, modified, and offered six iterations of two courses: "DNA" and "Computing for Poets". Larger percentages of women have consistently enrolled in these two courses vs. the traditional first course in the major. We share our open source course materials and present here our use of a blended learning classroom that leverages the increasing quality of online video lectures and programming practice sites in an attempt to maximize faculty-student interactions in class.

10. Kathleen Davis, Periodization and Sovereignty: How Ideas of Feudalism and Secularization Govern the Politics of Time Kathleen Davis, Periodization and Sovereignty: How Ideas of Feudalism and Secularization Govern the Politics of Time (pp. 405-407)

Index for 2011

Lexos 2017: building reliable software in python

Journal of Computing Sciences in Colleges, 2018

Refactoring software is challenging, but necessary to ensure software correctness and extensibili... more Refactoring software is challenging, but necessary to ensure software correctness and extensibility. We present a plan that blends automated tools and human reviews when refactoring the back-end of a web-based application. The Lexos software, developed by the NEH-funded Lexomics Project, provides a simple, web-based workflow for text processing, statistical analysis, and visualization of results when exploring digitized texts. The development of Lexos spans six years and includes over fifty undergraduate developers, many who assumed leadership roles in architectural design and systems engineering over three software releases. This paper shares our current refactoring effort on the Python backend to produce Lexos v3.2, an effort that includes a transition from Python v2.7 to Python v3.6. Good software engineering practices guide the effort, including the use of type hinting, a Model-View-Control pattern, PEP 8 code and PEP 257 documentation styles, unit testing, and continuous integr...

Lexos: An Integrated Lexomics Workflow

Digital Humanities Conference, 2017

Lexos is a browser-based suite of tools that helps lower barriers of entry to computational text ... more Lexos is a browser-based suite of tools that helps lower barriers of entry to computational text analysis for humanities scholars and students. Situated within a clean and simple interface, Lexos consolidates the common pre-processing operations needed for subsequent analysis, either with Lexos or with external tools. It is especially useful for scholars who wish to engage in research involving computational text analysis and/or wish to teach their students how to do so but lack the time for a manual preparation of texts, the skill sets needed to prepare their texts analysis, or the intellectual contexts for situating computational methods within their work. Lexos is also targeted at researchers studying early texts and texts in non-Western languages, which may involve specialized processing rules. It is thus designed to facilitate advanced research in these fields even for users more familiar with computational techniques. Lexos is developed by the Lexomics research group led by Michael Drout

Essay Bioinformatics and the Undergraduate Curriculum Essay

Recent advances involving high-throughput techniques for data generation and analysis have made f... more Recent advances involving high-throughput techniques for data generation and analysis have made familiarity with basic bioinformatics concepts and programs a necessity in the biological sciences. Undergraduate students increasingly need training in methods related to finding and retrieving information stored in vast databases. The rapid rise of bioinformatics as a new discipline has challenged many colleges and universities to keep current with their curricula, often in the face of static or dwindling resources. On the plus side, many bioinformatics modules and related databases and software programs are free and accessible online, and interdisciplinary partnerships between existing faculty members and their sup-port staff have proved advantageous in such efforts. We present examples of strategies and methods that have been successfully used to incorporate bioinformatics content into under-graduate curricula.

Introducing Students to Explorations of Digitized Texts Using Lexos

String Play with Regular Expressions

Perl for Exploring DNA, 2007

Meeting Report: Incorporating Genomics Research into Undergraduate Curricula

Cell Biology Education, 2002

In the first of two National Science Foundation (NSF)funded workshops, 30 professors of biology a... more In the first of two National Science Foundation (NSF)funded workshops, 30 professors of biology and computer science from 18 institutions met at Wheaton College in Norton, Massachusetts, on June 6-7, 2002, to share ideas on how to incorporate genomics research into undergraduate curricula. The participants included nine pairs or trios of biologists and computer scientists, anticipating or already implementing collaborations. In a before-and-after format, the two workshops are intended to encourage experimentation in the classroom (June 2002) followed by reflection on and evaluation of ideas (June 2003). Interdisciplinary work is the heart of any research in genomics. The magnitude of the data sets and the scale of the problems require the expertise of individuals from both computer science and biology or biochemistry . Collaborations in the sciences are common in many research settings but can be difficult to implement in undergraduate classrooms, especially in a relatively new field such as genomics. Biology students need opportunities to ask original questions and participate in algorithm and software design to learn how to set up new projects with programmers. Likewise, programmers entering the field of genomics must have a richer facility with the types of analyses and hypotheses that are useful, and programmers could benefit from interactions with biologists who will be using their programs. Our goals and objectives for this initial workshop targeted these needs and are listed in Table . Following is a discussion of the six main outcomes of the June 2002 workshop. From our perspective, one of the more significant outcomes of the first workshop was the overwhelming number of participants who left feeling more confident about their ideas and feeling justified that new teaching models are needed. The

Bioinformatics and the Undergraduate Curriculum

Cell Biology Education, 2010

Recent advances involving high-throughput techniques for data generation and analysis have made f... more Recent advances involving high-throughput techniques for data generation and analysis have made familiarity with basic bioinformatics concepts and programs a necessity in the biological sciences. Undergraduate students increasingly need training in methods related to finding and retrieving information stored in vast databases. The rapid rise of bioinformatics as a new discipline has challenged many colleges and universities to keep current with their curricula, often in the face of static or dwindling resources. On the plus side, many bioinformatics modules and related databases and software programs are free and accessible online, and interdisciplinary partnerships between existing faculty members and their support staff have proved advantageous in such efforts. We present examples of strategies and methods that have been successfully used to incorporate bioinformatics content into undergraduate curricula.

Classification and regression tree (CART) analyses of genomic signatures reveal sets of tetramers that discriminate temperature optima of archaea and bacteria

Archaea, 2008

Classification and regression tree (CART) analysis was applied to genome-wide tetranucleotide fre... more Classification and regression tree (CART) analysis was applied to genome-wide tetranucleotide frequencies (genomic signatures) of 195 archaea and bacteria. Although genomic signatures have typically been used to classify evolutionary divergence, in this study, convergent evolution was the focus. Temperature optima for most of the organisms examined could be distinguished by CART analyses of tetranucleotide frequencies. This suggests that pervasive (nonlinear) qualities of genomes may reflect certain environmental conditions (such as temperature) in which those genomes evolved. The predominant use of GAGA and AGGA as the discriminating tetramers in CART models suggests that purine-loading and codon biases of thermophiles may explain some of the results.

Of Dendrogrammatology: Lexomic Methods for Analyzing Relationships among Old English Poems

The Journal of English and …, 2011

The genome of every organism is composed of millions of small chemical units called nucleobases, ... more

Pattern Recognition through Computational Stylistics: Old English and Beyond

Lexomics: Integrating the research and teaching spaces

Teaching together: a three-year case study in genomics

Journal of Computing Sciences in Colleges, 2003

The emerging field of "Genomics" (the analysis of DNA sequences) requires interdiscipli... more The emerging field of "Genomics" (the analysis of DNA sequences) requires interdisciplinary collaborations between computer scientists and biologists. Whereas most colleges and universities do not and may not ever have full programs in bioinformatics/genomics, new models of teaching and associated supporting materials are needed if we are to provide undergraduate science majors with experiences in the art of cooperation necessary to solve tomorrow's problems in genomics. We report here on our recent three-year experiences with "linking" computer science and biology courses. By infusing genomics into existing computer science and biology courses ("Algorithms," "Software Engineering," "Genetics," and "Cell Evolution"), interdisciplinary classes and labs in genomics are provided to all computer science majors and over half of all majors in the biological sciences (biology, biochemistry, environmental science, and psychobio...

Doing Their Own Math: Computer Support of Discursive Approaches to "Real" Math Problems

Traditionally, there has been no obvious role for the computer in an elementarylevel classroom or... more Traditionally, there has been no obvious role for the computer in an elementarylevel classroom oriented toward "talking about math" as a way of deepening children's understanding of mathematical problem situations. We suggest that an appropriate computer learning environment can serve as a useful tool to both complement and be enhanced by discursive approaches to mathematics. In this paper we describe software, some of which is currently being tested in classrooms, which allows students to create and share word problems motivated by classroom discussion of an arithmetically relevant situation, and to dynamically explore links between linguistic and other symbolic representations of their problems and those of other children. In conjunction with the discursive approach, these facilities support pedagogical methods such as the integration of writing, science and mathematics; roles for students as knowledge contributors rather than as passive recipients; and a motivated u...

Toward Reproducibility in DH Experiments: A Case Study in Search of Edgar Allan Poe's First Published Work

Reproducing experimental results is a hallmark of empirical investigation and serves both to veri... more Reproducing experimental results is a hallmark of empirical investigation and serves both to verify and inspire. This paper is a call for more systematic documentation of computational stylistic experiments. Publishing only summaries of the methods and results of empirical work is an artifact of traditional print media. To facilitate experimental reproducibility and to help the growing community who wish to learn how to apply computational methods and subsequently teach the next generation of scholars, the publication of results must include (i) access to the digitized texts, (ii) a clear workflow and most essentially (iii) the source code that led to each and all of the experimental results. By way of example, we present the steps and process in a GitHub repository for computationally probing the unknown and contested authorship of an 1831 short story entitled “A Dream” as we seek evidence if this work is similar to other attributed works by Edgar Allan Poe. The entire framework is...

Lexos: An Integrated Lexomics Workflow

Lexos is a browser-based suite of tools that helps lower barriers of entry to computational text ... more Lexos is a browser-based suite of tools that helps lower barriers of entry to computational text analysis for humanities scholars and students. Situated within a clean and simple interface, Lexos consolidates the common pre-processing operations needed for subsequent analysis, either with Lexos or with external tools. It is especially useful for scholars who wish to engage in research involving computational text analysis and/or wish to teach their students how to do so but lack the time for a manual preparation of texts, the skill sets needed to prepare their texts analysis, or the intellectual contexts for situating computational methods within their work. Lexos is also targeted at researchers studying early texts and texts in non-Western languages, which may involve specialized processing rules. It is thus designed to facilitate advanced research in these fields even for users more familiar with computational techniques. Lexos is developed by the Lexomics research group led by Mi...

A DNA motif lexicon: cataloguing and annotating sequences

In Silico Biology, 2004

ABSTRACT: The rapid proliferation of genomic DNA sequences has created a significant need for sof... more

EngageCSEduMaking interdisciplinary connections to engage students

ACM Inroads