DEVELOPING AN EXPERIMENT MANAGEMENT SYSTEM

Miron Livny (*), Yannis Ioannidis (*), Gary G. Borisy (**), John M. Norman (***)

(***) Department of Soil Science

University of Wisconsin - Madison

CONTACT INFORMATION

Miron Livny
Computer Sciences Department
1210 W. Dayton St.
University of Wisconsin
Madison, WI 53706
Phone: (608) 262-0856
Fax : (608) 262-9777
Email: miron@cs.wisc.edu

WWW PAGE

http://www.cs.wisc.edu/ZOO

PROGRAM AREA

Virtual Environments

KEYWORDS

Experiment management, complex object visualization, visual queries, visual abstractions, visual translation specifications

PROJECT SUMMARY

This project has focused on developing the ZOO Desktop Experiment Management Environment (DEME) that will provide scientists with support for the management of long term experimental studies. Although our goal is for the system to be as generic as possible, special emphasis has been given to plant-growth simulation experiments in Soil Sciences and spectroscopy experiments in Biochemistry. The focus of our research has been on the following areas: prototyping pieces of the system, user-interfaces, data translation between objects in object-oriented databases and flat files, and communication with experimentation environments. Below, we briefly describe the technical results in each area and provide references to the relevant papers that we have co-authored.

Development

A prototype system based on the Moose object-oriented data model and the Fox declarative query language that we have designed has been partially developed on top of the Informix relational database system. The architecture of ZOO has been pretty much finalized and significant progress has been made in its implementation [1]. The system is at a stage where all of its modules are operational (in varying degrees of the final overall functionality desired). Specific details on the efforts on several of these modules are mentioned in the corresponding subsections below. The more advanced modules are being used by three domain scientists on the University of Wisconsin campus to design their experimental studies and the corresponding databases. Specifically, a large Soil Sciences experiment and a large NMR spectroscopy experiment are being captured as Moose schemas, with the ultimate goal of connecting the entire experimentation environments with ZOO. All users of the ZOO-related tools already developed have been enthusiastic about the prospects of having the complete ZOO system operational in their labs [2,3,4,5].

User Interfaces

One of the main research emphasis within this project has been on user-interfaces, and especially schema management. One of the most advanced and critical modules of ZOO is Opossum, a flexible, customizable, and extensible schema management system that approaches user-schema interaction in an innovative way [6]. It is based on a visualization formalism that we have introduced earlier, which separates the visual domain from the data domain and establishes a mapping (metaphor) between the two [7]. Opossum employees several novel techniques to offer the following capabilities: enhancement of schema visualizations with user-specific annotations, organizational information, and aesthetic preferences; exploration of schemas through choice of visual representations; and creation of new visual representation styles when existing ones prove unsatisfactory. Opossum is operational and is probably the module of ZOO most heavily used by our domain scientist collaborators. One of the most important characteristics of Opossum is its support for large visual schema layout. Motivated by the needs of our collaborators, we have developed techniques that strike a balance between user specification and automatic generation of layouts, work at multiple granularities, and are generally applicable. In particular, we have introduced a general framework and layout algorithm that (a) deals with arbitrary types of visual objects, (b) allows objects to be viewed in any one of several different visual representations (at different levels of detail), and (c) uses a small number of user-specified layouts to guide heuristic decisions for automatically deriving many other layouts in a manner that attempts to be consistent with the user's preferences [8]. The algorithm has been implemented within Opossum and has been rather effective in capturing the intuition of the scientists using the system.

Translation Between Object-Oriented Data and Flat Files

Another issue in ZOO that we have emphasized is the interaction of the system with external experimentation environments, in particular, simulators [9]. These simulators use flat files as their input (resp. output), which are generated based on (resp. generate) the corresponding Moose objects inside ZOO. This problem of translating database objects into a flat format to be written out in a flat Ascii file or, conversely, translating the contents of a file into a complex database object arises in several applications. In the context of ZOO, we have introduced Frog, a visual tool that can be used to specify translations between database objects and flat files, requiring no programming by the user. The tool can deal with objects of arbitrary complexity, without the object complexity being directly reflected in the complexity of the corresponding visual interaction. Based on the visual actions of the user, the tool stores enough information in a map-file, whose contents are used at run-time by another tool, Turtle, to translate any chosen database object into the appropriate file layout. These tool has been partially developed within ZOO and have been tried in a limited way by our collaborators with success.

PROJECT REFERENCES

[1] Y. Ioannidis, M. Livny, S. Gupta, and N. Ponnekanti, "ZOO: A Desktop Experiment Management Environment" , Proc. 22nd International VLDB Conference, Bombay, India, September 1996.

[2] J. L. Markley, J. B. Olson, Jr., R. Chylla, W. M. Westler, E. L. Ulrich, Y. Ioannidis, and M.Livny, "Approaches to Automating the Assignment of NMR Spectra of Proteins" (abstract), 37th Experimental NMR Conference, Asilomar, CA, March 1996.

[3] J. L. Markley, E. L. Ulrich, R. A. Chylla, M. Livny, Y. E. Ioannidis, J. B. Olson, D. Argentar, and W. M. Westler, "NMR Laboratory Process Control and Data Management" (abstract), 34th Annual Eastern Analytical Symposium, Somerset, NJ, November 1995.

[4] E. L. Ulrich, D. Argentar, M. Livny, Y. E. Ioannidis, J. L. Markley, "The NMR Dictionary" (abstract), mmCIF Workshop, American Crystallographic Association Meeting, Montreal, Canada, July 1995.

[5] E. L. Ulrich, M. Livny, Y. Ioannidis, C. Mortezai-Zanjani, A. Klimowicz, and J. L. Markley, "BioMagResBank" (abstract), Keystone Symposia, Frontiers of NMR in Molecular Biology - IV, Keystone, CO, April 1995.

[6] E. Haber, Y. Ioannidis, and M. Livny, "OPOSSUM: Desk-Top Schema Management through Customizable Visualization" , Proc. 21st International VLDB Conference, Zurich, Switzerland, September 1995, pp. 527-538.

[7] E. Haber, Y. Ioannidis, and M. Livny, "Formalizing Visual Metaphors in Any Dimension" (position paper), Proc. 2nd FADIVA Workshop, Glasgow, Scottland, July 1995.

[8] Y. Ioannidis, M. Livny, J. Bao, and E. Haber, "User-Oriented Visual Layout at Multiple Granularities" , Proc. 3nd International Workshop on Advanced Visual Interfaces, Gubbio, Italy, May 1996, pp. 184-193.

[9] V. Anjur, Y. Ioannidis, and M. Livny, "Frog and Turtle: Visual Bridges Between Files and Object-Oriented Data" , Proc. 8th International Conference on Scientific and Statistical Database Management, Stockholm, Sweden, June 1996.

AREA BACKGROUND

In the past few years, several scientific communities have initiated very ambitious and broad-ranged projects in their disciplines. The NASA Eos effort and the NIH Human Genome project are two examples of such national and international scientific endeavors. A major part of these projects is the collection of huge amounts of data (sometimes measured in petabytes) on complex phenomena. Managing this surge of scientific data poses significant challenges, many of which cannot be effectively addressed by existing database technology. This has resulted in much research activity in the area of Scientific Database Systems. Nevertheless, still little attention has been devoted to the needs of small teams of scientists who perform individual experimental studies in their laboratories. In particular, a major problem that many experimental scientists are facing is that there are no adequate experiment management tools that are powerful enough to capture the complexity of the experiments and at the same time are natural and intuitive to the non-expert. A small laboratory that can easily generate and store several megabytes of data per day is still dependent on the good old paper notebook when it comes to keeping track of the data. The experience of several researchers working in the area as well as our own experience from installed software (pieces of ZOO) as tested and evaluated in real-life settings has shown that one of the biggest challenges of experiment management environments like ZOO lies with their user interface. Thus, such systems are no different from general database systems, whose user interfaces have time and again been considered as (one of) the most important area(s) in need of research attention. The main problems faced by such systems are related to schema visualization, experiment flow modeling, visual query languages, visual queries, incremental queries, and others.

AREA REFERENCES

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RELATED PROGRAM AREAS

Adaptive Human Interfaces; Speech and Natural Language Understanding.

POTENTIAL RELATED PROJECTS

None currently.