Introduction to Science Informatics Lecture 1

What Is Science? a dependence on external verification; an expectation of reproducible results; a focus on falsifiable claims; the development of rich knowledge structures; a progressive refinement of that knowledge; etc. Sciences seem to share various characteristics: For more, see: Academics have debated this point for over a century, and it continues to arise both as a philosophical and as a practical matter (e.g., the case of Intelligent Design).

Science ≠ Philosophy emphasizes reason and argumentation as opposed to experimentation and observation; explores the development of concepts and the principles of knowing as opposed to explanations of phenomena and general predictive laws. Science and philosophy differ on standards of evidence and on the primacy of falsifiable claims. In particular, philosophy Nevertheless, philosophy can inform and inspire scientific activity, and science is a major topic of philosophical discussion.

Science ≠ Mathematics stresses theorems and conjectures, not laws and explanations; validates knowledge through logical proof as opposed to experiment and observation; emphasizes abstract objects in place of natural or artificial phenomena. Science and mathematics differ on standards of Evidence and on the subjects of produced knowledge. More specifically, mathematics However, scientists often employ mathematical tools.

Science ≠ Engineering study artifacts more so than the natural world; primarily produce these artifacts over knowledge; emphasize efficiency over novelty; and rely on logical proof and empirical evidence. Science and engineering often share methodology, but largely differ in their products. Notably, engineers Although engineering fields at times are accused of being applied science, they also produce rich knowledge of their own and include sciences of the artificial.

What Is Informatics? Informatics is an emerging field that designs, develops, and studies information-processing artifacts which:  store and retrieve content in memory;  draw inferences and predict outcomes;  make decisions and solve problems; and  interact and exchange information with others. Informatics is an interdisciplinary field driven by applications from science, law, public policy, and other domains. In studying and addressing the information needs of these fields, informatics scientists identify general principles of information use within social and interactive contexts.

Informatics ≠ Computer Science  problem-driven applications over theoretical analysis;  system-level innovation over algorithm refinement; and  user-oriented systems over stand-alone programs. Informatics uses the methods and technologies of computer science, but it favors These emphases lead to systems that enhance and augment human capabilities.

Informatics ≠ Information Science processes for storing information; processes for retrieving information; solutions for managing information; principles for organizing information; and techniques for transforming information. Although information science overlaps with informatics in many ways, it has traditionally studied information as separate from its consumers. The field focuses on Moreover, these topics may be studied without regard to the computational tools that play a large role in the field of informatics.

What Is Science Informatics? scientific data; scientific knowledge; scientific discovery; and scientific communities. Science informatics comprises the use of informatics technology to address scientific challenges and the use of scientific challenges to drive informatics research. This research area investigates four main topics: Advancements in science informatics can not only increase our understanding of the scientific process but also stimulate discovery in other scientific domains.

Scientific Data: Integration and Retrieval SciScope

Scientific Ontology and Taxonomy Formation Protégé

Scientific Modeling and Simulation Stella

Scientific Workflows Kepler

Scientific Discovery Environments Prometheus

Scientific Communications: Indexing and Retrieval CiteSeer

Expected Course Outcomes

Course Outline Introduction to science informatics Background material for science informatics Philosophy of science, cognitive science The scientific method Scientific data Collection, manipulation, visualization Scientific knowledge Taxonomies, laws, models, workflows

Course Outline Scientific discovery Scientific communities Literature, social networks Applications of science informatics DENDRAL, BLAST Open problems

Course Registration CPI 494: Enroll under this number for undergraduate credit CPI 598: Enroll under this number for graduate credit. Requires an additional individual project that (a) proposes a new informatics tool to support scientific research or (b) analyzes a historic episode of scientific discovery in computational terms Grade percentages are adjusted to accommodate this project. Refer to the syllabus.

Course Grading Grades for CPI 494 (CPI 598) are given based on multiple criteria, including Homework assignments: 40% (32%) Group project: 20% (16%) Class participation and discussion: 20% (16%) Final Exam: 20% (16%) (Individual research project: 20%) More information about the assignments will appear on the course website.

Homework Homework assignments account for 40% of the final grade and include exercises on scientific data scientific laws scientific models scientific discovery scientific literature These exercises will require the use of informatics tools to carry out scientific activities.

Group Project The group project accounts for 20% of the final grade. In general, your group should include between X and Y members, and students should form groups by (DATE). The project will involve the successive use of computational methods to store data, to model these observations, and to describe the results in a scientific paper.

Exams The final exam will account for 20% of the course grade and is scheduled for (DATE) (TIME) (LOCATION). Any changes will be announced in class and on the course website. (Will this exam be open book or open note?) (Is there also a midterm exam?)

General Information Course information is available from the course website and includes the syllabus, the course schedule, and a reading list with links to online papers. Visit the website regularly for any updates.

My Contact Information Name: Pat Langley Office: (LOCATION) Office Hours: (TIME)