Computing and the Love of Words
Collaborations in Genomics and the Digital Humanities
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Dr. Mark D. LeBlanc, Professor of Computer Science
Wheaton College, Norton, MA
cs.wheatoncollege.edu/mleblanc
Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
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made with BubbleViz
lexos3.wheatoncollege.edu
Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
A Computational Linguist, Math Educator, and
a Cognitive Scientist walk into a bar …
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Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
A Computational Linguist, Math Educator, and a Cognitive Scientist walk into a bar …
“Traditional wording”
In the beginning, Alex had some marbles. Then Bethany gave Alex 3 more marbles. Now Alex has 8 altogether. How many marbles did Alex have in the beginning?
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Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
A Computational Linguist, Math Educator, and a Cognitive Scientist walk into a bar …
“Traditional wording”
In the beginning, Alex had some marbles. Then Bethany gave Alex 3 more marbles. Now Alex has 8 altogether. How many marbles did Alex have in the beginning?
Below: a more tersely-worded version sometimes found on exams.
Alex had some marbles. Bethany gave Alex 3 marbles. Now Alex has 8. How many marbles did Alex have?
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Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
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1st and 3rd grader’s success rates on tests
LeBlanc, M.D. and Weber-Russell, S. (1996). Text integration and mathematical connections: a computer model of arithmetic word problem solving. Cognitive Science, v20(3), 357-407.
Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Me (by myself): My model “read” and solved word problems.
EDUCE (parser): 23,000 lines of LISP
SELAH (text integration/solver): 9,300 lines of LISP
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Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Lesson #1ab
Me (by myself): My model “read” and solved word problems.
EDUCE (parser): 23,000 lines of LISP
SELAH (text integration/solver): 9,300 lines of LISP
Math Ed: “The wording matters to kids.”
Cognition: “Where are your stats? How does the model’s memory load and required text-based inferences compare with children’s success rates?
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Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Lesson #1ab
Me (by myself): My model “read” and solved word problems.
EDUCE (parser): 23,000 lines of LISP
SELAH (text integration/solver): 9,300 lines of LISP
Math Ed: “The wording matters to kids.”
Cognition: “Where are your stats? How does the model’s memory load and required text-based inferences compare with children’s success rates?
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(b) ground truth matters
(a) clients matter!
Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Working with BIO: The Genomics Research Group
circa 1998
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Me (very naively):
Do you biologist have data?
Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Working with BIO: The Genomics Research Group
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Science, Volume 282, 11 Dec 1998
First multi-cellular organism sequenced
≅1000 cells
Six Chromosomes
Entire Genome: 101 M base pairs
Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
E.coli K12 genome (only 5M bp) on my Desktop
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% ls -l Ecoli.fna
-rw-r--r--+ 1 w00028110 523238136 4639298 Sep 14 2003 Ecoli.fna
Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
E.coli K12 genome
>gi|170079663|ref|NC_010473.1| Escherichia coli str. K-12, complete genome
AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA
TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC
ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG
CCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA
GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTG
AAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT
GACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTT
GCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC
TGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGT
TACTGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT
GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTCACCG
CCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGC
TGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGT …
TATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTG
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Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Lesson #2a
>gi|170079663|ref|NC_010473.1| Escherichia coli str. K-12, complete genome
AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA
TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC
ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG
CCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA
GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTG
AAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT
GACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTT
GCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC
TGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGT
TACTGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT
GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTCACCG
CCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGC
TGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGT …
TATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTG
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(a) Computer scientists have hubris.
Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Lesson #2ab
>gi|170079663|ref|NC_010473.1| Escherichia coli str. K-12, complete genome
AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA
TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC
ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG
CCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA
GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTG
AAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT
GACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTT
GCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC
TGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGT
TACTGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT
GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTCACCG
CCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGC
TGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGT …
TATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTG
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(a) Computer scientists have hubris.
(b) Be prepared to be WOWed!
Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Lesson #3: A good metaphor can take you a long way …
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Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Lesson #3: A good metaphor can take you a long way …
Imagine that you have the text of
Alice in Wonderland ...
(but remove all the spacing, word boundaries, etc.)
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Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Could we decipher Alice in Wonderland?
allrightsaidthecatandthistimeitvanishedquiteslowlybeginningwith theendofthetailandendingwiththegrinwhichremainedsometimeaftertherestofithadgone
irregular grammar
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Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Regulatory Motifs: On/Off switches for gene regulation
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+
-
gene
Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Regulatory Motifs: On/Off switches for gene regulation
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+
-
gene
Direct Repeats: ACGGacgg
Mirror Repeats: ACGTtgca
Inverted Repeats: ACGTacgt
Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Regulatory Motifs: On/Off switches for gene regulation
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+
-
gene
Wait!?
Like palindromes?
Direct Repeats: ACGGacgg
Mirror Repeats: ACGTtgca
Inverted Repeats: ACGTacgt
Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Palindromes? Really? Like …
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Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Palindromes? Really? Like …
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Yup.
Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Lesson #4: Ask your prof, “Now what?”
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Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
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Analysis by hand...
Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Analysis by hand...
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We can help!
1998-2017
Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
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Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
LeBlanc, M.D., Aspeslagh, G. ‘00, Buggia N. ‘01, and Dyer , B.D. (2000). An annotated catalogue of inverted repeats of Caenorhabditis elegans Chromosome III with observations concerning odd/even biases and conserved motifs, Genome Research, v10(9): 1381-1392.
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Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
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Dyer, B.D., LeBlanc, M.D., Benz, S. ‘05, Cahalan, P.’04, Donorfio, B.’04, Sagui, P. ’04, Villa, A.’03, and Williams, G. ‘03 (2004). A DNA motif lexicon: cataloguing and annotating sequences. In Silico Biology, v4, 0039. 471-478.
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Dyer, B.D., Kahn, M.J., and LeBlanc, M.D. (2007). Classification and regression tree (CART) analyses of genomic signatures reveal sets of tetramers that discriminate temperature optima of archaea and bacteria. Archaea 2:159–167.
Genomic signatures (counting “words”)
� teaching together
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COMP 215 Algorithms
BIO 211 Genetics
BIO/COMP 242 DNA
examples of
COMP 115 Python Programming
Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Course Materials (for other profs)
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LeBlanc, M.D. and Dyer, B.D. (2007). Perl for Exploring DNA. Oxford University Press.
LeBlanc, M.D. and Dyer, B.D. (2004). Bioinformatics and Computing Curricula 2001 -- Why Computer Science is well positioned in a post-genomic world. ACM SIGCSE Bulletin, v36 (4), Dec. 2004, 64-67.
https://www.engage-csedu.org/
1_DNA: Playing with (strings of) DNA
5_DNA: Comparative Genomics via Genomic Signature
Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Lesson #5: Got computational chops? You are needed more than ever!
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Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Lesson #5: Got computational chops? You are needed more than ever!
today:
Evo 2: a genome foundation AI model trained on over 9T DNA building blocks from 128,000 species
(the entire tree of life)
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Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
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Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Lesson #1: Clients matter; ground truth matters.
Lesson #2: Be prepared to be WOWed!
Lesson #3: A good metaphor can take you a long way …
Lesson #4: Ask your prof, “Now what?”
Lesson #5: Got computational chops? You are needed more than ever!
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Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Lesson #6: Be prepared to change course
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Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Lesson #6: Be prepared to change course
and knowing you can help others makes you feel good
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^
really
Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Lesson #6: Be prepared to change course
circa 2005
Mike Drout (English, Medieval, Tolkien scholar):
“Whoa! The entire (surviving) Anglo-Saxon (Old English) corpus
is on this CD-ROM!”
Me: “umm, cool.”
Drout: “Can you write programs to search for words?”
Me: (small sigh) “Yup. That’s pretty much what we do.”
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Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Lexomics: A new close reading ….
Summers: 2008 - present
8-15 compSci and Humanities students
Wheaton internal funding and
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Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Lexomics: A new close reading ….
Summers: 2008 - present
8-15 compSci and Humanities students
Wheaton internal funding and
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Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
From Whiteboard to Tools:
Corpus Construction with a Virtual Manuscript
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Pick from the Poetry
Pick from the Prose
Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
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Lexos - a workflow for experiments with digitized texts
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Beowulf: a very (very) close read …
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Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Building Tools for a close read: Rolling Window
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Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Feng, W. ’19 and LeBlanc, M.D. (2019). Top-10 Suggestions from a Decade of Managing Undergraduate Software Teams. The Journal of Computing Sciences in College, v34(6), 70-83.
Zhang, C. ’18, de Landaluce, A. ’17, Feng, W. ’19, Steffens, E. ’18, Kleinman, and LeBlanc (2018). Lexos 2017: Building Reliable Software in Python. The Journal of Computing Sciences in College, v33(6), 124-134.
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Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Top-10 Suggestions from a Decade of Managing Undergraduate Software Teams
Feng, W. ’19 and LeBlanc, M.D. (2019). Journal of Computing Sciences in College, v34(6), 70-83.
2.1 Recruit actively and iteratively
2.2 Proceed the initial sprint with a bootcamp
2.3 Use continuous integration (CI) tools
2.4 Use a good, modularized structure
2.5 Apply unit testing
2.6 Conduct peer reviews
2.7 Meet in daily stand-ups
2.8 Lead toward success: assign easy tasks early
2.9 Improve one tool
2.10 Add new functionalities
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Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Course Materials (for other profs)
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Boese, E.S., LeBlanc, M.D., and Quinn, B.A. (2017). EngageCSEdu: Making interdisciplinary connections to engage students. ACM Inroads, v8(2), 33-36.
2_Poets: Reading Poetry Backwards – RPB v1.0
4_Poets: True or False? Elves are tall … and Tolkien won’t let you think otherwise
5_Poets: Only in the Poetry - Searching the Anglo-Saxon Corpus
Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Lesson #7: Embrace hard, open-ended problems
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Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
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Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
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A Dream (1831) signed: “P”
Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
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LeBlanc, M.D. (2017). Toward Reproducibility in DH Experiments: A Case Study in Search of Edgar Allan Poe’s First Published Work. Digital Humanities 2017, Montreal, Canada, August 9, 2017 https://dh2017.adho.org/abstracts/027/027.pdf
Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
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Edgar
and brother Henry
Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
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Edgar
and brother Henry
Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
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Edgar?
and brother Henry
Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
IF (stuck) goto Lesson #1: Clients matter
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Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
IF (stuck) goto Lesson #1: Clients matter
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Ask a chatBot for help finding a domain expert?
Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
IF (stuck) goto Lesson #1: Clients matter
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omg! “Delvish” !!
Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Lesson #6: Be prepared to change course
Lesson #7: Embrace hard, open-ended problems
Lesson #1: Clients matter
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Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
Computing and the Love of Words
Collaborations in Genomics and the Digital Humanities
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Dr. Mark D. LeBlanc, Professor of Computer Science
Wheaton College, Norton, MA
cs.wheatoncollege.edu/mleblanc
Computer Science with Purpose: Humanities, Life Sciences, Social Sciences - Feb. 25, 2025
thank you
do we have time to play with Lexos?
lexos.wheatoncollege.edu
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