Diane Phylis Pozefsky

SNA Networks of Small Systems

This paper discusses SNA/LEN, a possible extension of Systems Network Architecture intended to allow peer, dynamic, and easy to use networking functions for a variety of node sizes down to and including the new generation of personal computers. After reviewing the special requirements posed by small systems and the need for including them as equal partners in networks, the LEN architecture is described. This is done by following a sequence of steps that begin when a logical resource at some node that may not yet be part of the connectivity of an existing network requests a session with a remote logical resource of unknown location. After connectivity with the preexisiting network is established, directory services locates the remote object, route selection services determines the preferred path, a session is activated, and deadlock-free flow control assures a useful flow of data. Preliminary quantitative results from an LEN prototype are presented.

Chembench: a cheminformatics workbench

MOTIVATION Advances in the field of cheminformatics have been hindered by a lack of freely available tools. We have created Chembench, a publicly available cheminformatics portal for analyzing experimental chemical structure-activity data. Chembench provides a broad range of tools for data visualization and embeds a rigorous workflow for creating and validating predictive Quantitative Structure-Activity Relationship models and using them for virtual screening of chemical libraries to prioritize the compound selection for drug discovery and/or chemical safety assessment. AVAILABILITY Freely accessible at: http://chembench.mml.unc.edu CONTACT alex_tropsha@unc.edu

iFold: a platform for interactive folding simulations of proteins

UNLABELLED We built a novel web-based platform for performing discrete molecular dynamics simulations of proteins. In silico protein folding involves searching for minimal frustration in the vast conformational landscape. Conventional approaches for simulating protein folding insufficiently address the problem of simulations in relevant time and length scales necessary for a mechanistic understanding of underlying biomolecular phenomena. Discrete molecular dynamics (DMD) offers an opportunity to bridge the size and timescale gaps and uncover the structural and biological properties of experimentally undetectable protein dynamics. The iFold server supports large-scale simulations of protein folding, thermal denaturation, thermodynamic scan, simulated annealing and p(fold) analysis using DMD and coarse-grained protein model with structure-based Gō-interactions between amino acids. AVAILABILITY http://ifold.dokhlab.org

Space-Efficient Storage Management in an Attribute Grammar Evaluator

A space-efficient strategy for storing attributes during evaluation of an attribute grammar is presented. Attributes are classified as either one-pass or multipass. One-pass attributes are stored on a pushdown stack, and their storage is freed when no longer needed. Examination of extant grammars shows that a vast majority of attributes are indeed one-pass, and therefore the scheme presented can greatly reduce the storage requirements of an attribute grammar evaluator. Several approaches to storage management for multipass attributes are also presented. Data for several grammars are collected and used to show the effectiveness of the proposed storage management scheme.

A Meta-Implementation for Systems Network Architecture

IBMs Systems Network Architecture (SNA) is formally defined by a meta-implementation program written in the Format and Protocol Language (FAPL). This paper describes the structure of the SNA meta-implementation and the development of FAPL. The most interesting aspect of the meta-implementation is that the architecture specification of SNA is itself machine executable. This property leads to a number of applications in software technology, such as automated protocol validation and direct Implementation from the formal specification.

Multiprotocol transport networking: eliminating application dependencies on communications protocols

The Multiprotocol Transport Networking (MPTN) architecture is a general solution that breaks the binding between distributed applications and communications protocols. The MPTN architecture enables existing applications to run unmodified over any communications protocol. In this paper, we first present the trends in networking that resulted in todays networks supporting multiple communications protocols. Next, we describe the classes of problems this support causes. The MPTN architecture is described and presented as a solution to many of these problems. We also present several alternative solutions to the multiple communications protocol problem and compare them to the MPTN solution. Last, we describe the IBM AnyNet™ family of products that implement the MPTN architecture.

Chembench: A Publicly Accessible, Integrated Cheminformatics Portal

The enormous increase in the amount of publicly available chemical genomics data and the growing emphasis on data sharing and open science mandates that cheminformaticians also make their models publicly available for broad use by the scientific community. Chembench is one of the first publicly accessible, integrated cheminformatics Web portals. It has been extensively used by researchers from different fields for curation, visualization, analysis, and modeling of chemogenomics data. Since its launch in 2008, Chembench has been accessed more than 1 million times by more than 5000 users from a total of 98 countries. We report on the recent updates and improvements that increase the simplicity of use, computational efficiency, accuracy, and accessibility of a broad range of tools and services for computer-assisted drug design and computational toxicology available on Chembench. Chembench remains freely accessible at https://chembench.mml.unc.edu.

Multiprotocol transport networking: a general internetworking solution

The multiprotocol transport networking (MPTN) architecture proposed in this paper is a general solution to providing interconnectivity for applications. The MPTN architecture provides a protocol-independent system interface that includes most functions provided by existing transport protocols. As a result, the MPTN architecture decouples higher-layer protocols, application programming interfaces, and applications from protocols at the transport layer and below. Using the MPTN architecture, current and new applications can function unmodified over any transport supported under the MPTN interface. In addition, MPTN transport-layer gateways provide an end-to-end communication facility across a number of networks running different protocols. Therefore, a collection of networks running different protocols can serve as a single logical network.<<ETX>>

SNA's design for networking

Systems Network Architecture (SNA) provides users with services needed in a networking environment: sharing of communication lines, directory services, connection establishment, improved reliability, management services, and an appropriate interface and set of facilities for distributed programming. It provides these services within the scope of a layered architecture that has evolved to the rich, set-functions and products that it supports. The major concepts of SNA are reviewed. The three major functions that a network provides-transporting data, enabling distributed programming, and application-level services-are discussed.<<ETX>>

Multi-Descriptor Read Across (MuDRA): A Simple and Transparent Approach for Developing Accurate Quantitative Structure–Activity Relationship Models

Multiple approaches to quantitative structure-activity relationship (QSAR) modeling using various statistical or machine learning techniques and different types of chemical descriptors have been developed over the years. Oftentimes models are used in consensus to make more accurate predictions at the expense of model interpretation. We propose a simple, fast, and reliable method termed Multi-Descriptor Read Across (MuDRA) for developing both accurate and interpretable models. The method is conceptually related to the well-known kNN approach but uses different types of chemical descriptors simultaneously for similarity assessment. To benchmark the new method, we have built MuDRA models for six different end points (Ames mutagenicity, aquatic toxicity, hepatotoxicity, hERG liability, skin sensitization, and endocrine disruption) and compared the results with those generated with conventional consensus QSAR modeling. We find that models built with MuDRA show consistently high external accuracy similar to that of conventional QSAR models. However, MuDRA models excel in terms of transparency, interpretability, and computational efficiency. We posit that due to its methodological simplicity and reliable predictive accuracy, MuDRA provides a powerful alternative to a much more complex consensus QSAR modeling. MuDRA is implemented and freely available at the Chembench web portal ( https://chembench.mml.unc.edu/mudra ).