Peter Friedland

The concept and implementation of skeletal plans

A new method for automated planning, refinement of skeletal plans, has been developed for the problem of experiment design in the domain of molecular biology. The method resulted from a study of the problem-solving behavior of scientists which showed that design usually consisted of look-up of abstracted plans followed by hierarchical plan-step refinement. The skeletal plan method has been implemented through two generations of problem-solving systems, the second generation involving a synthesis with the metaplanning approach of Stefik.

Knowledge-based simulation of genetic regulation in bacteriophage lambda.

We have developed a general-purpose computer program for the functional simulation of regulatory genetics. This simulator is knowledge-based and was developed using the Unit System, a software tool for the acquisition, representation, and manipulation of hierarchically organized knowledge. The advantages of a knowledge-based design are presented, and the simulators architecture is described. Its performance on the decision between lytic and lysogenic growth in Bacteriophage Lambda is reported.

SEQ: a nucleotide sequence analysis and recombination system

SEQ is an interactive, self-documenting computer program that contains procedures for the analysis of nucleotide sequences and the manipulation of such sequences to allow the simulation and prediction of the results of recombinant DNA experiments.

Discovering the Secrets of DNA

Sophisticated software tools are becoming increasingly important in helping biologists understand how nature operates. Symbolic pattern-recognition and artificial-intelligence methodologies are contributing to the development of such software.

BIONETtm: national computer resource for molecular biology

This paper describes briefly the BIONET National Computer Resource for Molecular Biology. This presentation is intended as information for scientists in molecular biology and related disciplines who require access to computational methods for sequence analysis. We describe the goals, and the service and research opportunities offered to the community by BIONET, the relationship of BIONET to other national and regional resources, our recent efforts toward distribution of the resource to BIONET Satellites, and procedures for investigators to gain access to the Resource.

Intelligent computational assistance for experiment design.

We have developed an automated system for the design of laboratory experiments in molecular biology. The system uses a planning method known as skeletal plan refinement that attempts to emulate the human cognitive task of experiment design. This paper describes the theory, history, and implementation of the design system and illustrates its function in the domain of DNA cloning experiments.

GENESIS, a knowledge-based genetic engineering simulation system for represntation of genetic data and experiment planning

We have built a knowledge-based genetic engineering simulation system-- GENESIS-- capable of representing both domain-specific and general knowledge. Information is stored within a hierarchically-organized framework composed of structures called units. A series of sophisticated editors enables no-computer specialist molecular geneticists to construct a knowledge base through direct interaction with the computer. Three types of knowledge specific to the domain of molecular genetics, MAPS, sequences and RULES are discussed in detail with examples.

MAXAMIZE. A DNA sequencing strategy advisor

The MAXAMIZE advisory system determines from user-provided restriction maps an optimal strategy to do nucleotide sequencing by methods involving end-labeled fragments. The maps may be either simple linear restriction maps of fragments or complex circular maps including restriction sites of a vector. The whole system is interactive and is written in the Genetic English language provided by the GENESIS System, a molecular genetics knowledge representation and manipulation package. In addition, MAXAMIZE provides bookkeeping facilities for sequencing and offers advise on how to verify the newly obtained sequence data.

The 2008 Classic Paper Award: Summary and Significance

We at the NASA laboratory believed that our best work came when we simultaneously advanced AI theory and provided immediately usable solutions for current NASA problems. “Solving Large-Scale Constraint Satisfaction and Scheduling Problems Using a Heuristic Repair Method,” by Steve Minton, Mark Johnston, Andy Phillips, and Phil Laird clearly achieved both. It proved that local search and repair was applicable to a wide class of constraint satisfaction problems and clearly explicated the theory behind that proof.

Intelligent Assistance for Complex Systems

Complex systems are becoming more pervasive, yet in order for these systems to be used effectively, machine-based assistance is needed. With the advent of powerful personal systems it is anticipated that experts in various disciplines will become increasingly dependent on computational environments provided they are given a means of exploiting system capabilities. Traditional help systems have made use of canned text which is presented in response to typing a “?” or “help”. Many integral help systems embed canned hints at appropriate places in the program. Help is commonly provided via a scheme for accessing text files. Help files may be indexed by names such as MAIL, EDIT, LOGIN. Indexing of files is sometimes extended by permitting the user to type a sequence of words such as HELP MAIL READ to provide assistance on subcategories of a topic. Canned text can also be accessed hierarchically through use of a menu system. Most traditional help systems use one of the techniques described to provide assistance.