Xinformatics Spring 2012

View Source Code of "Xinformatics Spring 2012"

<strong>Instructor</strong>: <a href="http://tw.rpi.edu/web/person/PeterFox">Professor Peter Fox</a> - foxp at rpi dot edu
<strong>TA</strong>: Abigail Fuller - fullea6 at rpi dot edu
<strong>Meeting times</strong>: Tuesday morning 9:00 am - 11:50 am.
<strong>Office Hours</strong>: Monday 2:00-3:00pm in <a href="http://tw.rpi.edu/web/Contact">Winslow</a> 2120 or by appointment in JRSC 1W06
<strong>phone</strong>: 518-276-4862
<strong>Class Listing</strong>: ITEC 4962/6961  53353/53354, ERTH 4963/6963  53355/53356, CSCI 4960/6960  53357/53358
<strong>Class Location</strong> JEC 3207

==Description==

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. 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. 24): Introduction to informatics - <document href="Xinformatics2012_week1.ppt" alt="Week 1 slides"/>
* Week 2 (Jan. 31): Information systems theory - <document href="Xinformatics2012_week2.ppt" alt="Week 2 slides"/>
* Week 3 (Feb. 7): Foundations; semiotics, library, cognitive and social science and class exercise - information modeling   - <document href="Xinformatics2012_week3.ppt" alt="Week 3 slides"/>
* Week 4 (Feb. 14): Capturing the problem: Use case development and requirement analysis - <document href="Xinformatics2012_week4.ppt" alt="Week 4 slides"/>
* Week 5 (Feb 21): Class presentations for assignment 1
* Week 6 (Feb. 28): Class presentations continued and Information architectures intro and design - <document href="Xinformatics2012_week6.ppt" alt="Week 6 slides"/>
* Week 7 (Mar. 6): Information architectures theory and practice continued (Internet, Web, Grid, Cloud) project definitions <document href="Xinformatics2012_week7.ppt" alt="Week 7 slides"/>
* Mar. 13: no classes - spring break 
* Week 8 (Mar. 20): Information Integration, Life-cycle and Visualization - <document href="Xinformatics2012_week8.ppt" alt="Week 8 slides"/>
* Week 9 (Mar. 27): Information Management, Workflow, and Discovery, Project definition check-in/ discussion - <document href="Xinformatics2012_week9.ppt" alt="Week 9 slides"/>
* Week 10 (Apr. 3): A worked example - atmospheric informatics <document href="Xinformatics2012_week10.ppt" alt="Week 10 slides"/>
* Week 11 (Apr. 10): Information Audit and Material review - what you need to remember - <document href="Xinformatics2012_week11.ppt" alt="Week 11 slides"/>
* Apr. 17: no class - Grand Marshall week 
* Week 12 (Apr. 24):   State-of-the-Art examples;  Astroinformatics - [[Media:astroinformatics.pptx|slides]], geoinformatics [[Media:astroinformatics.pptx|slides]], Cheminformatics - [[Media:tbd.pptx|slides]] 
* Week 13 (May 1):  Final project presentations

==Reading/ Assignment/ Reference List==

'''Class 1''' Reading Assignment: Xinformatics Applications - State of the Art
* Clinical Informatics: [http://www.himss.org/ASP/topics_clinicalInformatics.asp]
* Clinical Informatics, Medical Device Connectivity: [http://www.himss.org/CI_Insights/HIMSSClinicalInformaticsInsights.asp?date=20091012]]
* 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]
* Astro Informatics: [http://arxiv.org/abs/0909.3892],  [http://www.practicalastroinformatics.org/conferences/aas10]  
* 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]

'''Class 2''': Reading Assignment: Information theory

* [http://en.wikipedia.org/wiki/Information_entropy Information entropy]
* [http://www.lecb.ncifcrf.gov/~toms/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://nlp.stanford.edu/IR-book/information-retrieval-book.html Information retrieval] 
* [http://compression.ru/download/articles/huff/huffman_1952_minimum-redundancy-codes.pdf Compression and encoding: D.A. Huffman, "A Method for the Construction of Minimum-Redundancy Codes", Proceedings of the I.R.E., September 1952, pp 1098–1102]
* [http://en.wikipedia.org/wiki/Abductive_reasoning Abductive reasoning]

'''Class 3''': Reading Assignment: Foundations, semiotics, ...

* [http://cm.bell-labs.com/cm/ms/what/shannonday/shannon1948.pdf Shannon]
* [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]
* [http://topquadrantblog.blogspot.com/2011/09/ontologies-and-data-models-are-they.html Information Models - Conceptual, Logical and Physical]
* optional [http://www.cspeirce.com/ Peirce]
* [http://cogsci.uwaterloo.ca/courses/phil256.html]
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC131031/]
* [http://www.slideshare.net/jahendler/social-machines-oxford-hendler Social Machines]
* [http://www.wbemsolutions.com/tutorials/CIM/index.html CIM]
* [http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.61.2749&rep=rep1&type=pdf Presentation]
* [http://www.sofsem.cz/sofsem07/addon/ewt.2.2.ppt Personalization in presentation systems]

<document href="Xinformatics2012_Assignment1.pdf" alt="Assignment 1"/>

'''Class 4''': 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/wiki.tw/images/4/48/UseCase-Template_SeS_Fall2008.doc Use case template]
**[http://tw.rpi.edu/wiki.tw/images/a/ad/UseCase-SensorWeb-semantics_fox20080324.doc Partial use case example 1]
**[http://tw.rpi.edu/wiki.tw/images/0/03/UseCase-Volcano_Atmosphere_fox20080410.doc Partial use case example 2]

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

<document href="Xinformatics2012_Assignment2.pdf" alt="Assignment 2"/>

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

Next week
* [http://www.ibm.com/developerworks/library/us-inarch.html Architecture]
* [http://www.webmonkey.com/2010/02/information_architecture_tutorial/ Architecture]
* [http://www.worqx.com/color/ Color]
* [http://colorschemedesigner.com/ Color Scheme Designer website]

[http://tw.rpi.edu/wiki.tw/images/9/93/Xinformatics2011_Assignment_3.pdf Assignment 3]

'''Class 6''':  Reading Assignment:
* [http://www.oracle.com/technology/architect/entarch/pdf/architectural_strategies_for_cloud_computing.pdf Cloud architecture considerations]
* [http://www.greatreality.com/color/ColorGuess.htm Color Theory]

'''Class 7''': Reading Assignment:
* [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]
* [https://www1.ietf.org/rfc/rfc1958.txt Internet architecture]

<document href="Xinformatics2012_Assignment_Project.pdf" alt="Final Assignment Project"/>

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

'''Information Integration'''

* Social issues in information discovery and sharing: [http://ctovision.com/2008/04/information-discovery-and-sharing/], [http://odni.gov/reports/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]

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

'''Information Discovery''' 

* Information discovery graph(IDG): [http://www.google.com/url?sa=t&source=web&ct=res&cd=24&ved=0CBUQFjADOBQ&url=http%3A%2F%2Fciteseerx.ist.psu.edu%2Fviewdoc%2Fdownload%3Fdoi%3D10.1.1.41.5456%26rep%3Drep1%26type%3Dpdf&ei=XZfUS8SwLcOqlAeV5LjtDA&usg=AFQjCNFVmFXpQAO_s4gmWxQbYk3KE0OJVQ&sig2=PfkftJRHc3LVH_fVEUSFEA]
* 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.theappgap.com/using-twitter-for-information-discovery.html]

'''Metadata'''

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

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

* None

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

* Wikipedia entry for Information Audit: [http://en.wikipedia.org/wiki/Information_audit]
* Information Audit: [http://www.librijournal.org/pdf/2003-1pp23-38.pdf]

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

* None

==Objectives==

* 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.

==Course Learning Objectives==

Through class lectures, practical sessions, written and oral presentation assignments and projects, students should:
* Understand and develop skill in Development and Management of multi-skilled teams in the application of Informatics
* Understand and know how to develop Conceptual and Information Models and Explain them to non-experts
* Knowledge and application of Informatics Standards
* 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

==Topics for Xinformatics/ Foundations:==

* Introduction to informatics
* State-of-the-Art examples; bioinformatics
* 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 and Workflow Management
* Information Discovery, Information Integration

==Xinformatics 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

== 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.   If you have any question concerning this policy before submitting an assignment, please ask for clarification. 

==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 6961-01)
*or permission of the instructor

==Attendance Policy==

Enrolled students may miss at most one class without permission of the instructor.
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View Source Code of "Xinformatics Spring 2012"
