Arthur P. Goldberg

VirtualPlant: A Software Platform to Support Systems Biology Research

Data generation is no longer the limiting factor in advancing biological research. In addition, data integration, analysis, and interpretation have become key bottlenecks and challenges that biologists conducting genomic research face daily. To enable biologists to derive testable hypotheses from the increasing amount of genomic data, we have developed the VirtualPlant software platform. VirtualPlant enables scientists to visualize, integrate, and analyze genomic data from a systems biology perspective. VirtualPlant integrates genome-wide data concerning the known and predicted relationships among genes, proteins, and molecules, as well as genome-scale experimental measurements. VirtualPlant also provides visualization techniques that render multivariate information in visual formats that facilitate the extraction of biological concepts. Importantly, VirtualPlant helps biologists who are not trained in computer science to mine lists of genes, microarray experiments, and gene networks to address questions in plant biology, such as: What are the molecular mechanisms by which internal or external perturbations affect processes controlling growth and development? We illustrate the use of VirtualPlant with three case studies, ranging from querying a gene of interest to the identification of gene networks and regulatory hubs that control seed development. Whereas the VirtualPlant software was developed to mine Arabidopsis (Arabidopsis thaliana) genomic data, its data structures, algorithms, and visualization tools are designed in a species-independent way. VirtualPlant is freely available at www.virtualplant.org.

Restoring consistent global states of distributed computations

We present a mechanism for restoring any consistent global state of a distributed computation. This capability can form the baais of support for rollback and replay of computations, an activity we view aa essential in a comprehensive environment for debugging distributed programs. Our mechanism records occasional state checkpoints and logs all messages communicated between processes. Our mechanism offers flexibility in the following ways: any consistent global state of the computation can be restored; execution can be replayed either exactly as it occurred initially or with user-controlled variations; there is no need to know a prioti what states might be of interest. In addition, if checkpoints and logs are written to stable storage, our mechanism can be used to restore states of computations that cause the system to crash.

High-level language support for programming distributed systems

A strategy for simplifying the programming of heterogeneous distributed systems is presented. The approach used is based on integrating a high-level distributed programming model, the process model, directly into programming languages. Distributed applications written in such languages are portable across different environments, are shorter, and are simpler to develop than similar applications developed using conventional approaches. The process model is discussed, and Hermes and Concert/C, two languages that implement this model, are described. Hermes is a secure, representation-independent language designed explicitly around the process model. Concert/C is the C language augmented with a small set of extensions to support the process model while allowing reuse of existing C code. Hermes has been prototyped: an implementation of Concert/C is in development.<<ETX>>

Optimistic failure recovery for very large networks

Optimistic failure recovery mechanisms are proposed as a way to provide transparent fault tolerance to distributed applications and systems. The authors identify problems that may arise when these mechanisms are applied to vast networks including many processors and spanning large geographical areas and many administrative domains. They present a technique-recovery unit gateways-that can be used to address many of these issues with existing failure recovery algorithms. This method can be applied with minimal disruption to existing transparent recovery systems, as well as to build large optimistic recovery systems while minimizing the dependency tracking overhead.<<ETX>>

Hermes language experiences

We recount and examine experiences with Hermes, an experimental language for programming distributed systems. Hermes has several unusual language features, including compile‐time checking of data initialization, representation independent data aggregates, and an integrated process model. To facilitate compile‐time initialization checking, Hermes stores data in tables and does not expose pointers. We study these features in light of the experiences of Hermes users around the world, analyzing the strengths and weaknesses of the language.