Plaster Source Code

This document contains the source code for program Plaster. Before attempting to read this one should become familiar with the Plaster User\u27s Guide. The first routine listed below is the main program, which contains an overview of the entire system, many internal and installation notes, and an index of the routines which follow. The remaining user routines called by Plaster follow in alphabetical order. After these come all the Include files referenced by the routines

Plaster Users\u27 Guide

Creating graphics for TV and storage tube displays is common and easy at most computer installations today. It is less easy to produce high-quality hard-copy of graphics for publication. This manual describes a program called Plaster which produces a raster representation of a picture created with the PlotlO graphics package for display on the Santec S700 printer. Plaster (PlotlO to Raster) thus allows one to obtain hard-copy of an image created with the prevalent and easy to use PlotlO language on the inexpensive but high quality Santec printer

Call for an enzyme genomics initiative

I propose an Enzyme Genomics Initiative, the goal of which is to obtain at least one protein sequence for each enzyme that has previously been characterized biochemically. There are 1,437 enzyme activities for which Enzyme Commission (EC) numbers have been assigned but no sequence can be found in public protein-sequence databases

Many Genbank Entries for Complete Microbial Genomes Violate the Genbank Standard

A survey of Genbank entries for complete microbial genomes reveals that the majority do not conform to the Genbank standard. Typical deviations from the Genbank standard include records with information in incorrect fields, addition of extraneous and confusing information within a field, and omission of useful fields. This situation results from two principal causes: genome centres do not submit Genbank records in the proper form and the Genbank, EMBL and DDBJ staffs do not enforce the database standards that they have defined

Web-based metabolic network visualization with a zooming user interface

<p>Abstract</p> <p>Background</p> <p>Displaying complex metabolic-map diagrams, for Web browsers, and allowing users to interact with them for querying and overlaying expression data over them is challenging.</p> <p>Description</p> <p>We present a Web-based metabolic-map diagram, which can be interactively explored by the user, called the <it>Cellular Overview</it>. The main characteristic of this application is the zooming user interface enabling the user to focus on appropriate granularities of the network at will. Various searching commands are available to visually highlight sets of reactions, pathways, enzymes, metabolites, and so on. Expression data from single or multiple experiments can be overlaid on the diagram, which we call the Omics Viewer capability. The application provides Web services to highlight the diagram and to invoke the <it>Omics Viewer</it>. This application is entirely written in JavaScript for the client browsers and connect to a Pathway Tools Web server to retrieve data and diagrams. It uses the OpenLayers library to display tiled diagrams.</p> <p>Conclusions</p> <p>This new online tool is capable of displaying large and complex metabolic-map diagrams in a very interactive manner. This application is available as part of the Pathway Tools software that powers multiple metabolic databases including <monospace>Biocyc.org</monospace>: The Cellular Overview is accessible under the <monospace>Tools</monospace> menu.</p

Collaborative Proposal: Form and function of phytoplankton in unsteady, low Reynolds-number flows

Small-scale flow dynamics at low Reynolds numbers (Re) are important to phytoplankton cells in delivery of nutrients, sensory detection by and physical encounter with herbivores, accumulation of bacterial populations in the phycosphere or region immediately surrounding phytoplankton cells and coagulation of cells themselves as a mechanism terminating blooms. In nature most phytoplankton experience unsteady flows, i.e., velocities near the cells that vary with time due to the intermittency of turbulence and to discontinuous, spatially distributed pumping by herbivores. This unsteadiness has not previously been taken into account in models or measurements with plankton. Moreover, there have been decade- and century- long lags in moving relevant models of unsteady flow effects at low Re from applied mathematics and engineering to ecological applications. Engineering models show unsteady effects due to the history of formation of spatially extensive flow perturbations or wakes should be important to unsteady motions of moderately small biota. This project will address these affects. Non-swimming phytoplankton, and in particular diatoms, will be used as the simplest case where important unsteady flow behaviors should arise. This research activity will include a multi-level educational program, aimed at graduate research assistants, undergraduate research interns, undergraduate marine sciences majors and high-school teachers. Low-Re behaviors afford unusual opportunities to experience how mathematics, physics and biology inseparably catalyze understanding of phenomena that run counter to intuition. This activity will also include international collaborations with world experts on organism-flow interaction in Cambridge (T.J. Pedley) and Copenhagen (T. Kiorboe & A.W. Visser). The overall goals of the activity are to accelerate the flow of understanding from modelers to measurers to users of the information and back again. Educational materials that project U.S. national standards will be developed during intensive summer workshops with the high-school teachers and be made available on the web. Unsteady flow effects on phytoplankton will be predicted with explicit models based on singularity solutions (that involve the useful simplification that force is applied to the fluid at a small number of points) and mathematical models that include both the near field at low Re and the far field over a range of Re, both representative of nature. Singularity solutions allow explicit treatment of the role of complex cell shapes. Scaled-up analog models will be placed in a large Couette vessel to better visualize behaviors for both the research and teaching efforts. Natural-scale, but simplified, unsteady flows will be produced in smaller Couettes (nested, counter-rotating cylinders with seawater in the gap between the two cylinders) containing live phytoplankton and will be quantified by magnifying, particle-imaging velocimetry (PIV). Image analysis will be used to measure translation, rotation and flexural deformation of the phytoplankton. These studies will test various hypotheses derived from the general thesis that cell shapes and mechanical properties interact with unsteady flows to produce potentially fitness-enhancing, relative motions of the cell or chain and its surrounding fluids. A basic hypothesis is that unsteady fluid motion will interact with bending of cells to produce relative motion of fluid and phytoplankter. A very exciting prospect is that periodic instabilities known to arise at low Re may allow flexible organisms to act as self-organizing engines - through elasticity to harness energy from decaying turbulence and thereby move relative to the fluid. It is also expected that this study of passively bending structures in unsteady flows will help to understand the use of flexible appendages in swimming. The work is likely to aid significantly in associating functions with the shapes and spines of microplankton that are used in the identification of fossil specimens. By including relevant, unsteady fluid motions at low Re, the study will also provide firmer linkages between form and function in living plankton in the size range from 10 - 1000 mm that many large phytoplankton, invertebrate and fish larvae and other small zooplankton occupy

CMG Collaborative Research: Interactions of Phytoplankton with Dissipative Vortices

The aim of this project is to develop coordinated laboratory experiments and computational models to address a fundamental question in oceanography concerning magnitudes and mechanisms of turbulence effects on phytoplankton and other particles at the spatial scale of individual organisms. The importance of external energy in the form of turbulence in determining relative success of different kinds of phytoplankton dates to the seminal analysis of Munk and Riley (1952) and Margalef (1978). Margalef\u27s mandala asserts that high nutrient concentrations and turbulence intensities favor dominance by diatoms, whereas low values favor non-red-tide dinoflagellates. Subsequent work has revealed a wide spectrum of turbulence effects among species of dinoflagellates, including growth stimulation. The physicochemical mechanisms that govern these effects largely remain to be determined, however.Through iteration between innovative numerical models and experiments, the investigators will close a growing gap between textbook understanding of turbulent flows and understanding of consequences for suspended organisms and particles. Models and experiments have used one-dimensional shear to assess turbulence effects at the level of single cells and chains. Effects of fluid straining on concentration fields and cell rotation have been predicted, and effects on cell growth and motion, documented. Current understanding of turbulence, however, places greater emphasis on vorticity, gradients in vorticity and vortices at dissipation scales experienced by individual phytoplankton cells. We propose to develop a framework for both numerical and analog evaluation of effects that cells experience from being in and near viscous-scale vortices, that capture effects of vorticity as well as fluid deformation, evolution of concentration fields, and fluid-structure interactions. Roles of vorticity and gradients in vorticity in determining cell motions and thereby shaping concentration fields have been underappreciated, partly because a signature feature of turbulence, i.e., vortex stretching, is impossible in the two-dimensional flows that so far have been used as theoretical models and the primary basis of analog devices.Numerical approaches will use two simplified models of small-scale vortex structure and evolution, the Burgers vortex and the Lundgren stretched-spiral vortex, giving particular attention to diffusion of vorticity within and away from both. Both decaying and equilibrium vortices will be explored. Models of cells and chains of cells will be based on shapes and flexural stiffnesses of actual cells and chains. Each will be placed successively at a range of positions within and near a vortex and will be fully coupled mechanically to the fluid. Behaviors of interest are cell and chain translation, rotation and deformation and their feedbacks to local velocity and vorticity fields that could be used by grazers to locate a cell. Also to be modeled is the diffusion of scalars (nutrients with cell as sink or metabolites with cell as source), allowing calculation of diffusive fluxes for nutrient acquisition and prediction of chemical fields used by grazers. The investigators will further take advantage of their existing models of flow around flagella to include motile dinoflagellates in the modeling and measurement scheme.Analog experiments will exploit the fact that flows near Kolmogorov scale are dominated by viscosity, just as in earlier Couette experiments, but will incorporate realistic, 3D time variation. Borrowing from a burgeoning variety of geometries used in microfluidics, the investigators will construct a variety of small devices that utilize shed vortex streets, mild jets and cavity flows to match deformation rates, vorticities and gradients in them that produce interesting effects on phytoplankton in their numerical models of vortices. These analogs will be used to test the model predictions and to pose new questions of the models.Broader impacts: Results for phytoplankton extend easily to other important phenomena such as diffusion of attractants from eggs spawned in a turbulent environment (e.g., by abalone and other benthic invertebrates) and corresponding sperm swimming capabilities. They have implications for other important encounter processes such as particle coagulation and sedimentation, hydrosol filtration, and predator-prey interactions. This new approach provides both a natural bridge from larger-scale, direct numerical simulation (DNS) models of turbulence to these individual-scale effects of turbulence and a logical path to parameterizing these effects in larger-scale fluid dynamic models.Turbulence intensity is one of the parameters most likely to be influenced by climate change, and the investigators will work closely with the Center for Ocean Sciences Education Excellence Ocean Systems (COSEE-OS) that has chosen oceans under climate change as its major focus. They will also build on their history of providing teaching and outreach materials in biomechanics at low Reynolds numbers for graduate students, undergraduates and high-school teachers. They will complement both of these efforts with professionally produced, evocative visual animations of the important phenomena that they identify for incorporation into the COSEE-OS website

The Pathway Tools cellular overview diagram and Omics Viewer

The Pathway Tools cellular overview diagram is a visual representation of the biochemical network of an organism. The overview is automatically created from a Pathway/Genome Database describing that organism. The cellular overview includes metabolic, transport and signaling pathways, and other membrane and periplasmic proteins. Pathway Tools supports interrogation and exploration of cellular biochemical networks through the overview diagram. Furthermore, a software component called the Omics Viewer provides visual analysis of whole-organism datasets using the overview diagram as an organizing framework. For example, gene expression and metabolomics measurements, alone or in combination, can be painted onto the overview, as can computed whole-organism datasets, such as predicted reaction-flux values. The cellular overview and Omics Viewer provide a mechanism whereby biologists can apply the pattern-recognition capabilities of the human visual system to analyze large-scale datasets in a biologically meaningful context. SRI's BioCyc.org website provides overview diagrams for more than 200 organisms. This article describes enhancements to the overview made since a 1999 publication, including the automatic layout capability, expansion of the cellular machinery that it includes, new semantic zooming and poster-generating capabilities, and extension of the Omics Viewer to support painting of metabolites, animations and zooming to individual pathway diagrams