Xinformatics 2018

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Instructor: Prof. Peter Fox - pfox at cs dot rpi dot edu
Course: Xinformatics: ERTH/CSCI/ITWS 4400/ 4600 CRNs: 53829, 53830, 53829. 53830, 53827, 53828
TA: Eliyah Afzal - afzale at rpi dot edu
Meeting times: Tuesday 3:00 pm - 5:50 pm.
Office Hours: By appointment in Winslow 2120 or Lally 207A
Phone: N/A
Class Location Lally 102

Description

In the last decade, Informatics has attained greater visibility across a broad range of disciplines, especially in light of great successes in bio- and biomedical-informatics and significant challenges in the dramatic increase of data and information resources. Xinformatics is intended to provide both the common informatics knowledge as well as how it is implemented in specific disciplines, e.g. X=astro, geo, chem, urban, econ, etc. Informatics' theoretical basis arises from information science, cognitive science, social science, library science as well as computer science. As such, it aggregates these studies and adds both the practice of information processing, and the engineering of information systems. This course will introduce informatics, each of its components and ground the material that students will learn in discipline areas by coursework and project assignments.

Syllabus/ Calendar (tentative)

Refer to Reading/ Assignment/ Reference list for each week (see below).

* Week 1 (Jan. 16): Introduction to informatics - Week 1 slides [Download]
* Week 2 (Jan. 23): Capturing the problem: Use case development and requirement analysis - Week 2 slides [Download]
* Week 3 (Jan. 30): Information systems theory - Week 3 slides [Download]
* Week 4 (Feb. 6): Foundations; semiotics, library, cognitive and social science - Week 4 slides [Download]
* Week 5 (Feb. 13): information Integration, Life-cycle and Visualization - Week 5 slides [Download]
* Feb. 20: no class - Tuesday follows Monday schedule
* Week 6 (Feb. 27): Information modeling (+class exercise), Information architecture: theory and practice/ design (Internet, Web, Grid, Cloud) Week 6a slides [Download]
* Week 7 (Mar. 6): Class presentations for assignment 3 and Project definitions Week 7 slides/ teams
* Mar. 13: no classes - spring break
* Week 8 (Mar. 20): Guest lectures on Informatics - stay tuned
* Week 9 (Mar. 27): Unstructured Information, Information Audit and Integrity, Workflows and Project Check-in Week 9 slides
* Week 10 (Apr. 2): Semantics of Information Quality and Bias, Information Retrieval and Project Check-in Week 10 slides
* Week 11 (Apr. 9): Global Change Information System and Project Check-in Week 11 slides
* Week 12 (Apr. 16): TBD Week 12 slides
* Week 13 (Apr. 23): Final project presentations. Final project due (written).

Reading/ Assignment/ Reference List

'''Class 1''' Reading Assignment: Xinformatics Applications
* Clinical and Bio-Informatics: [Bioinformatics: https://www.sciencedaily.com/releases/2016/12/161216142612.htm]
* Clinical informatics: [https://jclinbioinformatics.biomedcentral.com/articles/10.1186/2043-9113-5-S1-A1]
* Bio Informatics: [http://www.wired.com/wiredscience/2008/07/researchers-tra/]
* Biomedical informatics for proteomics [http://www.nature.com/nature/journal/v422/n6928/full/nature01515.html?free=2]
* Urban Informatics: [http://www.creativeclass.com/creative_class/2009/04/09/now emerging-urban-informatics/]
* Geo Informatics: [http://www.geoinformatics.com/blog/online-articles/spatial-developments-in-3d-4d-and-5d]
* Geoinformatics - choose a chapter from [https://books.google.com/books?hl=en&lr=&id=OHbGKCsZbwQC&oi=fnd&pg=PR5&dq=geoinformatics&ots=t1S_7ofEhG&sig=8OIpD_F8uAL9YrumlZ4JmeXycEg#v=onepage&q=geoinformatics&f=false]
* Geoinformatics - choose a chapter from [https://books.google.com/books?hl=en&lr=&id=OHbGKCsZbwQC&oi=fnd&pg=PR5&dq=geoinformatics&ots=t1S_7ofEhG&sig=8OIpD_F8uAL9YrumlZ4JmeXycEg#v=onepage&q=geoinformatics&f=false]
* Geoinformatics: [https://www.omicsonline.org/open-access/gis-applications-for-assessing-spatial-distribution-of-boreholes-and-handdug-wells-in-boroboro-community-atiba-local-government-oy-2469-4134-1000208.php?aid=93844]
* Astro Informatics: [http://arxiv.org/abs/0909.3892], [http://www.practicalastroinformatics.org/conferences/aas10]

'''Class 2''': Reading Assignment: Use case development and requirement analysis

Required:
* [http://en.wikipedia.org/wiki/Use_case] ,
* [http://alistair.cockburn.us/index.php/Use_cases,_ten_years_later]
* Reference
** [http://tw.rpi.edu/media/latest/UseCaseTemplate.docx Use case template]
** Partial use case example 1 [Download]
** Partial use case example 2 [Download]

Optional:
*[http://members.aol.com/acockburn/papers/AltIntro.htm]
*[http://alistair.cockburn.us/index.php/Resources_for_writing_use_cases]
*[http://alistair.cockburn.us/Usecasesintheoryandpractice180.ppt]
*[http://alistair.cockburn.us/Agileusecases1dy.ppt]
*[http://alistair.cockburn.us/index.php/Structuring_use_cases_with_goals]
*[http://www.foruse.com/publications/bibliographies/usecases.htm]
*[http://en.wikipedia.org/wiki/Use_case]
*[http://www.ddj.com/dept/architect/184414701]

Assignment 1 [Download]

'''Class 3''': Reading Assignment: Information theory

* [http://en.wikipedia.org/wiki/Information_entropy Information entropy]
* [https://schneider.ncifcrf.gov/information.is.not.uncertainty.html Information Is Not Entropy, Information Is Not Uncertainty!]
* [http://danielwilkerson.com/entropy.html More on entropy]
* [http://jitm.ubalt.edu/XIX-3/article2.pdf Context]
* [http://spectrum.ieee.org/tech-talk/telecom/internet/bell-labs-looks-at-claude-shannon-legacy-future-of-information-age?bt_alias=eyJ1c2VySWQiOiAiMmQ2YWM1NGItMzBkMi00NmUxLTgwNzItNTRhMzc3ZjBkNjg3In0%3D&utm_source=Tech%20Alert&utm_medium=Email&utm_campaign=TechAlert_05-19-2016 Claude Shannon and the Information Age]

'''Class 4''': Reading Assignment: Foundations, semiotics, ...

* [http://www.bayes.it/pdf/Shannon_1948.pdf Shannon's 1948 paper]
* [http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.93.714&rep=rep1&type=pdf Awareness in Context-Aware Information Systems]
* GUI ICON Sets [http://www.hongkiat.com/blog/40-free-and-useful-gui-icon-sets-for-web-designers/]
* [http://www.ccrnp.ncifcrf.gov/~toms/sequencelogo.html Sequence logos]
* [http://www.helsinki.fi/science/commens/dictionary.html Peirce in his words]
* [http://www.umbertoeco.com/en/semiotics-links.html Eco's Semiotics Links]
* [https://en.wikipedia.org/wiki/Semiotics Wikipedia entry for Semiotics]
* [http://cogsci.uwaterloo.ca/courses/phil256.html Cognitive Science (reference)]
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC131031/ Informatics Research Agenda and people]
* [http://en.wikipedia.org/wiki/Abductive_reasoning Abductive reasoning]
* optional [http://www.cspeirce.com/ Peirce]

Assignment 2 [Download]

'''Class 5''': Reading Assignment:

'''Information Integration'''

* Social issues in information discovery and sharing: [http://ctovision.com/2008/04/information-discovery-and-sharing/], [http://www.dni.gov/files/documents/Newsroom/Reports%20and%20Pubs/IC_Information_Sharing_Strategy.pdf]
* Information integration in geo-informatics [http://www.isi.edu/integration/TerraWorld/]
* [http://cseweb.ucsd.edu/~goguen/projs/data.html]
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1839387/]

'''Information Life Cycle'''

* [http://msdn.microsoft.com/en-us/library/bb288451.aspx MSDN Information Life Cycle]
* [http://searchstorage.techtarget.com/sDefinition/0,,sid5_gci963635,00.html Information Life Cycle definition and context]
* [http://www.computerworld.com/s/article/79885/The_new_buzzwords_Information_lifecycle_management]
* [http://www.databasejournal.com/sqletc/article.php/3340301/Database-Archiving-A-Critical-Component-of-Information-Lifecycle-Management.htm]
* [http://en.wikipedia.org/wiki/Information_Lifecycle_Management]
* [http://msdn.microsoft.com/en-us/library/bb288451.aspx]

'''Information Visualization'''

* [http://mastersofmedia.hum.uva.nl/2011/04/18/the-simple-ways-of-information-visualization/comment-page-1/]
* [http://www.siggraph.org/education/materials/HyperVis/domik/folien.html]
* [http://www.visual-literacy.org/periodic_table/periodic_table.html]

'''Information model development and visualization'''

* [http://www.acm.org/crossroads/xrds7-3/smeva.html]

'''Outside the current box'''
* Peter Fox and James Hendler, 2011, Changing the Equation on Scientific Data Visualization, Science, Vol. 331 no. 6018 pp. 705-708, DOI: 10.1126/science.1197654 online at http://www.sciencemag.org/content/331/6018/705.full or see: [http://escience.rpi.edu/publications/visualization/fox_hendler_science2011.html]

Assignment 3 [Download]

'''Class 6''': Reading Assignment:
* [http://topquadrantblog.blogspot.com/2011/09/ontologies-and-data-models-are-they.html Information Models - Conceptual, Logical and Physical]
* Application of information models: Xiaogang Ma, Jin Guang Zheng, Justin C. Goldstein, Stephan Zednik, Linyun Fu, Brian Duggan, Steven M. Aulenbach, Patrick West, Curt Tilmes, Peter Fox 2014, Ontology engineering in provenance enablement for the National Climate Assessment, Environmental Modelling and Software, 16, 191-205. doi: http://dx.doi.org/10.1016/j.envsoft.2014.08.002
* [http://www.webmonkey.com/2010/02/information_architecture_tutorial/ Architecture]
* [http://www.enterprise-architecture.info/Images/Defence%20C4ISR/enterprise_architecture_reference_models_v0_8.pdf Enterprise Architecture Reference Models]
* [http://en.wikipedia.org/wiki/Grid_computing Design considerations for the Grid]
* [http://www.w3.org/TR/webarch/ Architecture of the Web]
* [http://www.itu.int/ITU-T/worksem/ngn/200505/presentations/s1-meyer.pdf Internet architecture]
* [http://www.architecturewiki.com.au/DesignTheory Architectural Design Theory]
* [http://www.digital-web.com/types/design_in_theory_and_practice Design Theory in Practice - Web]
* [http://www.worqx.com/color/ Color]
* [http://colorschemedesigner.com/ Color Scheme Designer website]
* [http://www.greatreality.com/color/ColorGuess.htm Color Theory]

Assignment 4 [Download]

'''Class 7''': Reading Assignment:

* Final Assignment Project

'''Class 8''': Reading Assignment:

* [http://nlp.stanford.edu/IR-book/information-retrieval-book.html Information retrieval]

'''Class 9''': Reading Assignment:

"Unstructured"
* Unstructured Information [http://www.zdnet.com/blog/service-oriented/unstructured-data-the-elephant-in-the-big-data-room/7116]
"Audit"
* Wikipedia entry for Information Audit: [http://en.wikipedia.org/wiki/Information_audit]
* Information Audit: [http://www.librijournal.org/pdf/2003-1pp23-38.pdf]
*UIMA: [http://www.ibm.com/developerworks/data/downloads/uima/]
"Workflow"

'''Class 10''': Reading Assignment:

'''Information Discovery'''

* Information discovery graph(IDG)
* projects using information discovery: [http://www.nist.gov/itl/iad/rg/content-based-access.cfm]
* Information discovery and Library Sciences: [http://libtechtalk.wordpress.com/2009/01/12/information-discovery-via-the-library-catalog/]
* Information Discovery and retrieval tools : [http://ftp.rta.nato.int/public//PubFullText/RTO/EN/RTO-EN-026///EN-026-03.pdf]
* Social Search : [http://www.bothsidesofthetable.com/2010/12/20/the-power-of-twitter-in-information-discovery/]

'''Retrieval'''

* http://en.wikipedia.org/wiki/Metadata
* http://www.niso.org/publications/press/UnderstandingMetadata.pdf
* http://dublincore.org/

"Knowledge Representation"
* SPAR ontologies [http://opencitations.wordpress.com/2010/10/14/introducing-the-semantic-publishing-and-referencing-spar-ontologies/]
* SPAR discussion - semantic re-structuring of content [http://tw.rpi.edu/web/inside/ideas/SPAREvaluation]

'''Class 11''': Reading Assignment:

* None

'''Class 12''': Reading Assignment:

* None

'''Class 13''': Reading Assignment:

* N/A

Topics for Xinformatics/ Foundations:

* Introduction to informatics
* State-of-the-Art examples;
* Capturing the problem: Use case development and requirement analysis
* Information theory, models, tools
* Foundations; semiotics, library, cognitive and social science
* Information life-cycle
* Information architectures (Internet, Web, Grid, Cloud)
* Information Visualization,
* Information Audit and Workflow Management
* Information Discovery, Information Integration

Informatics Applications:

* Geoinformatics
* Astroinformatics
* Cheminformatics
* Bioinformatics
* Helioinformatics
* Health informatics
* Ecoinformatics

Xinformatics Project options (examples):

* Information Management for collaborative web sites
* Information Modeling for Health Sciences: Patient Records
* Information Architecture Analysis Case Study: GEOSS
* Information Management for Disasters: Earthquakes
* Information Content, Content and Structure Analysis: Library Information Systems

Suggested Prerequisites

*Knowledge such as that gained in a Data Base class (e.g., CSCI-4380)
*Knowledge such as that gained in a Data Structures class (e.g., CSCI-1200)
*Knowledge such as that gained in a Data Science class (e.g. ITEC/CSCI/ERTH 4350/6350)
*or permission of the instructor

Attendance Policy

Enrolled students may miss at most one class without permission of the instructor. Attendance partially counts toward the participation grade for this course.


Professors: Peter Fox

Course Numbers:
  • 53829, 53830, 53829. 53830, 53827. 53828
Description:
This course will introduce informatics, each of its components and ground the material that students will learn in discipline areas by coursework and project assignments. In the last 2-3 years, Informatics has attained greater visibility across a broad range of disciplines, especially in light of great successes in bio- and biomedical-informatics and significant challenges in the explosion of data and information resources. Xinformatics is intended to provide both the common informatics knowledge as well as how it is implemented in specific disciplines, e.g. X=astro, geo, chem, etc. Informatics' theoretical basis arises from information science, cognitive science, social science, library science as well as computer science. As such, it aggregates these studies and adds both the practice of information processing, and the engineering of information systems.
To instruct future information architects how to sustainably generate information models, designs and architectures To instruct future technologists how to understand and support essential data and information needs of a wide variety of producers and consumers For both to know tools, and requirements to properly handle data and information Will learn and be evaluated on the underpinnings of informatics, including theoretical methods, technologies and best practices.
Goal:
To instruct future information architects how to sustainably generate information models, designs and architectures To instruct future technologists how to understand and support essential data and information needs of a wide variety of producers and consumers For both to know tools, and requirements to properly handle data and information Will learn and be evaluated on the underpinnings of informatics, including theoretical methods, technologies and best practices.
Learning Objective:
hrough class lectures, practical sessions, written and oral presentation assignments and projects, students should: Develop and demonstrate skill in Development and Management of multi-skilled teams in the application of Informatics Develop Conceptual and Information Models and explain them to non-experts Demonstrate the application information theory and design principles to information systems Demonstrate knowledge and application of Informatics Standards Develop and demonstrate skill in Informatics Tool Use and Evaluation
Assessment Criteria:
Via written assignments with specific percentage of grade allocation provided with each assignment Via oral presentations with specific percentage of grade allocation provided Via group projects and presentations Via participation in class (not to exceed 10% of total) Graduate students are assessed on identified components per assignment. Undergraduates may complete graduate components for extra credit Late submission policy: first time with valid reason – no penalty, otherwise 20% of score deducted each late day
Academic Integrity:
Student-teacher relationships are built on trust. For example, students must trust that teachers have made appropriate decisions about the structure and content of the courses they teach, and teachers must trust that the assignments that students turn in are their own. Acts, which violate this trust, undermine the educational process. The Rensselaer Handbook of Student Rights and Responsibilities defines various forms of Academic Dishonesty and you should make yourself familiar with these. In this class, all assignments that are turned in for a grade must represent the student’s own work. In cases where help was received, or teamwork was allowed, a notation on the assignment should indicate your collaboration. Submission of any assignment that is in violation of this policy will result in a penalty. If found in violation of the academic dishonesty policy, students may be subject to two types of penalties. The instructor administers an academic (grade) penalty, and the student may also enter the Institute judicial process and be subject to such additional sanctions as: warning, probation, suspension, expulsion, and alternative actions as defined in the current Handbook of Student Rights and Responsibilities. First violation for a specific assignment will result in a zero grade. Second violation will result in failure of the course. If you have any question concerning this policy before submitting an assignment, please ask for clarification.