waashk/acm huggingface dataset:
information processing by cells and biologists (abstract only)  the core agenda of post-wwii molecular biology has been defined as the molecular understanding of how genetic information was transmitted and read out (see for example stent 1968), and, by the 1950's, the analogy between the tape in a turing machine and the linear sequence of nucleotides in dna was apparent to both computer scientists and biologists.  in the early 21st century, it may be that molecular biology can fruitfully return to these roots, by recasting part of its agenda in terms of the need to understand how biological information is processed. in a somewhat more modern formulation, cells can be though of as machines that process and make decisions on three kinds of information: 1) information stored in the genome 2) information about intracellular events (for example from heckpoint mechanisms) and 3) information external to the cell.  in many cases the machinery that cells use to make decisions is reasonably well understood at a qualitative level. however, in no case do we possess a corresponding quantitative understanding, and, reflecting this, nor are we very capable of predicting the outcomes of perturbations to the genome, the internal workings of the cell, or its external environment.  one path to understanding the behavior of these ensembles of components clearly lies in construction of mechanism-based quantitative models representing cellular processes. building such models requires solution of numerous computational and experimental biological challenges. i will detail some of these.  another path may involve computation on the qualitative biological knowledge that now exists. expert biologists reason on this qualitative information to make statements about the consequences of perturbations, but expert systems that do the same in the main do not exist. here, although the need is clear, the relative opacity (to me) of much of the seemingly relevant computer science literature has made it more difficult to figure out first steps.  finally, note that information theory (shannon 1948) has its roots in the 20th century need to understand transmission of electrical signals through channels. it is not immediately clear that the representations of biological processes used by biologists map well to concepts that come from this theory. to give only one example, one is hard pressed to define or find, inside a cell that is processing signals from the outside, either the signal or the "bits" (tukey, 1946) that might make it up. there may be thus be an opportunity here for new theory to guide thinking and further experiment.  roger brent
efficient optimal design space characterization methodologies  one of the primary advantages of a high-level synthesis system is its ability to explore the design space. this paper presents several methodologies for design space exploration that compute all optimal tradeoff points for the combined problem of scheduling, clock-length determination, and module selection. we discuss how each methodology takes advantage of the structure within the design space itself as well as the structure of, and interactions among, each of the three subproblems. (cad)  stephen a. blythe robert a. walker
design automation - lessons of the past, challenges for the future  during the past two decades, we have learned that design automation is increasingly the only viable way to deal with the complexity of electronic circuits. and da will continue to thrive in the future because of ever- increasing complexity.  following the development of the transistor and the integrated circuit, electronic desings grew almost exponentially in numbers of components and interconnections. unfortunately, so did the design effort and the potential for errors, as unwelcome effects. the automation of electronic designs attacked this complexity to save labor and improve quality. my company, bell labs, designs hundreds of vlsi chips each year and thousands of circuit packs. without design automation there is no way we could dot it---not in the required time and not with the available resources. without da, for example, designing and debugging our 32-bit microprocessor would have been virtually impossible.  john s. mayo
comparative analysis of organelle genomes, a biologist's view of computational challenges (abstract only)  with genomic data (generated by classical, functional, structural, proteo- and other `omic' approaches) accumulating at a stupendous rate, there is an ever increasing need for the development of new, more efficient and more sensitive computational methods. to highlight aspects of our computational needs, we will present results that emerged from the comparative genome analysis of mitochondria. having originated from an alpha- proteobacterial endosymbiont, these eukaryotic organelles contain small and extremely variable genomes, and are thus perfect model systems for the much more complex eubacterial and archaeal genomes. we are currently in vestigating mitochondrial dnas (mtdnas) in a lineage of unicellular, primitive protistan eukaryotes, the jakobids, with the aim to understand the evolution of mitochondrial genomes, genes and their regulation. because these organisms are difficult to grow, biochemical approaches aimed at understanding gene regulation are laborious, thus it is possible to capitalize considerably from predictions on genome and gene organization, and regulatory elements. contrary to approaches in which molecular data (gene order, sequence similarities) are used to infer the phylogenetic relationships among a group of organism, we know their phylogeny and employ this information to identify and model more or less conserved genetic elements and structural rna genes that are difficult to spot by conventional methods, in a phylogenetic-comparative approach.  franz lang
using our resources to improve publications  "we do it that way because we've always done it that way…"  due to the rapid advances in computer technology, many of us in academic computing are finding ourselves in the position of looking for ways to use this technology to improve those publications that we produce for general distribution. there are new concepts, new software packages and hardware that can now be utilized. one can't help but feel the excitement in our new-found ability to design, format, and produce a professional looking publication without depending on a professional printer. through the use of a word processing package, a desktop publisher and a laser printer, a whole new world has opened up to us.  academic computing publications at ball state university include a quarterly newsletter and mini-course schedule. for the last several years, there has basically been one person in charge of these publications. publishing the newsletter consisted of writing articles, collecting articles from other staff members, editing all articles, getting them formatted and printed by the secretary, cutting and pasting into newsletter form, and finally, sending the finished copy to the on-campus print shop. the mini- course schedule was produced in this same manner. we restructured our publication method to increase staff involvement and also, we made what seemed like almost a quantum leap to desktop publishing, computer graphics and staff production, making most of these changes between issues.  our original goals were to minimize cutting and pasting, to involve more staff and to produce a professional set of publications which would be more readable and helpful to the individual user. in so doing, we had to learn a lot of new things very quickly: new software, new hardware and---just as important---new ideas. one outcome was the many favorable comments we received from the academic community on the revised format of our mini-course schedule.  we feel that our presentation is to show that it is possible to make a dramatic change in production methods, given the right attitudes of acceptance, and willingness to utilize new resources: computer, personal, and personnel. we had to overcome more than just technical changes \---the greater challenge was in forming these concepts and new ideas.  pam claspell kathy sawyer
dora:: cad interface to automatic diagnostics  this paper will discuss a family of cad tools supporting automatic diagnosis and the usage of those tools in western electric company (weco) testing. the cad tools described in this paper are part of a package developed at the engineering research center (erc), princeton, new jersey. the diagnostic organization and retrieval algorithms (dora) system is a complex of programs which provide audited test programs and diagnostic data files from the results of lamp (logic analyzer for maintenance planning)1 circuit simulation. dora supports manufacturing and repair test facilities in all divisions of western electric that produce circuit packs or digital custom devices. improved engineering productivity in bell laboratories and western electric, efficient use of capital intensive test hardware, and reduced diagnostic costs are the goals of this package.  r. w. allen m. m. ervin-willis r. e. tulloss
computer budgeting of mineral holdings for a small scale mining operation  this paper describes how a computer program handles the problems encountered in developing a mining budget from a large number of individual and widely scattered ore deposits. among the difficulties overcome by the use of the program are constantly changing production forecasts requiring reworking of the budget, scheduling of the capacities of the offsite loading facilities, production rates requiring the mining of several properties concurrently while still maintaining quality control, and pressing time limits on several leases.  daniel l. mcculley
enhancement of the interaction between low-intensity r.f. e.m. fields and ligand binding due to cell basal metabolism  power absorption by biological tissues, due to low-intensity electromagnetic exposure at radio frequencies, as those generated by personal telecommunication systems, is typically negligible. nevertheless, the electromagnetic field is able to affect biological processes, like the binding of a messenger ion to a cell membrane receptor, if some specific conditions occur. the depth of the attracting potential energy well of the binding site must be comparable with the radio frequency photon energy. the dependance of the binding potential energy on the spatial coordinates must be highly non- linear. the ion--receptor system, in absence of the exogenous electromagnetic exposure, must be biased out of thermodynamic equilibrium by the cell basal metabolism. when the above conditions concur a low-intensity radio frequency sinusoidal field is able to induce a steady change of the ion binding probability, which overcomes thermal noise. the model incorporates the effects of both thermal noise and basal metabolism, so that it offers a plausible biophysical basis for potential bioeffects of electromagnetic fields, e.g., those generated by mobile communication systems.  b. bianco a. chiabrera e. moggia t. tommasi
some computer aided engineering system design principles  engineering design is a human activity which is becoming increasingly reliant on computer systems programmed to support design processes. the builders of such computer aided engineering (cae) systems have many problems to solve and this paper looks at some of the principles involved.  a model capable of describing the work of the designer is proposed and placed in the context of computer systems. this model is then used to classify basic design activities and leads to a set of computer aided engineering system design principles. an application of these principles is illustrated by a description of some of the methods used by the authors in designing computer aided electronic engineering products.  henry l. nattrass glen k. okita
the real world of design automation - part iii or the user's viewpoint chairman's introduction (panel discussion)  for the past two years, this panel examined design automation as professionals evaluating our own profession. with tongue only slightly in cheek, we discussed "a funny thing happened on the way to implementation" in 1978, and "adapting to the joys of madness" in 1979. both sessions were hard-hitting self appraisals of the way we do business. this year we elected to include a new element in "the real world of design automation": the user. too frequently, we become blinded by the brilliance of our own creation. we fail to recognize the reason for our existance. the user is, after all, the bottom line in design automation. our future depends on his successor failure.  p. losleben
hypercube data analysis in astronomy: optical interferometry and millisecond pulsar searches  astronomical data sets are beginning to live up to their name, in both their sizes and the complexity of the analysis required. here we discuss two astronomical data analysis problems which we have begun to implement on a hypercube concurrent processor environment: the intensive image processing required in an optical interferometry project, and the large scale power spectral analysis required by a search for millisecond-period radio pulsars. in both cases the analysis proceeds largely in the fourier domain, and we find that the problems are readily adapted to a concurrent environment. in the following report, we outline briefly the astronomical background for each problem, then discuss the general computational requirements, and finally present possible hypercube algorithms and results achieved to date.  p. gorham t. prince s. anderson
atm switch design by high-level modeling, formal verification and high-level synthesi  asynchronous transfer mode (atm) has emerged as a backbone for high-speed broadband telecommunication networks. in this paper, we present atm switch design, starting from a parametric high-level model and debugging the model using a combination of formal verification and simulation. the model has been used to synthesize atm switches according to customers' choices, by choosing concrete values for each of the generic parameters. we provide a pragmatic combination of simulation, model checking, and theorem proving to gain confidence in the atm switch design correctness.  s. p. rajan m. fujita k. yuan m. t-c. lee
college guidance counselor (abstract only)  an expert system for choosing a college has been developed using the insight 2+ rule-based tool on an at-compatible microcomputer. this expert system uses three categories in the selection process: admissions data, including sat score and class rank; the desired major; and personal preferences. the system uses the information to narrow down a list of colleges. at each stage, the user is given the option either to reduce the list through more questions or to choose directly from the list. the user can request various information about the colleges on the final list. design and implementation issues will be discussed including a comparison with a database-oriented design alternative.  t. reid l. r. medsker
graphic design tips for desktop publishers  since the introduction of the macintosh, the laserwriter, and pagemaker and the subsequent ability to create camera-ready or near-camera-ready documents on our desktops, document writers have found it necessary to become document designers as well. yet, this entails a number of choices. for example, what style or size of type? how many columns? where should headings be placed? should there be illustrations? if so, how should they be arranged? because most of us haven't been trained to make these choices, too often the result is badly designed and ineffective documents.  however, by understanding some of the basic principles of graphic design, even design novices can use a desktop publishing system to improve the way their documents look and, more importantly, make them more readable and more understandable. research has shown that certain design techniques dramatically expand a reader's capacity for information. in this session i will offer a number of simple design guidelines for creating effective desktop published documents and avoiding the common design pitfalls of overzealous desktop publishers without design training.  using before and after examples, i will discuss the graphic design choices available to desktop publishers and explain the best choices. topics will include choosing and using type styles and sizes, column width, capitals and italics, alignment, leading, word and letter spacing, white space, and balance to create effective memos, brochures, manuals, flyers, and newsletters.  good graphic design is more than a simple list of do's and don'ts. by explaining the reasons for certain design choices, i hope that those who attend this session will leave with a basic understanding of graphic design that they can use as a resource when designing their own desktop-published documents and as a basis for further study in graphic design if they are interested.  kenneth e. gadomski
the emerging technology of cad/cam  computer-aided design and manufacture (cad/cam) represents a merging of technological advances in computer hardware and software with pressing needs in manufacturing industries. integrated manufacturing systems--from computer graphics-aided design through engineering analysis and automated fabrication-- are only now beginning to fulfill nearly twenty-five-year old promises of increased production efficiency. this paper summarizes cad/cam's evolution and its current state and then describes some areas that will experience significant change in the next decade.  larry lichten
an object-oriented kernel for an integrated design and process planning system  an object-oriented kernel that integrates design and process planning in the domain of mechanical parts is presented. the kernel has identified and separated the integral elements of its domain from the elements that are associated with a particular design/manufacturing environment. consequently, it can be customized to a wide range of environments and be used as a rapid prototyping tool. a prototype has been developed and implemented in smalltalk-80.  s. j. feghhi m. marefat r. l. kashyap
inside risks: risks in medical electronics  the risks forum has had many accounts of annoying errors, expensive breakdowns, privacy abuses, security breaches, and potential safety hazards. however, postings describing documented serious injuries or deaths that scan be unequivocally attributed to deficiencies in the design or implementation of computer-controlled systems are very rare. a tragic exception was a series of accidents which occurred between 1985 and 1987 involving a computer-controlled radiation therapy machine.  jonathan jacky
imposing specificity by regulated localization (abstract only)  many biologically important enzymes --- rna polymerases, rna splicing enzymes, ubiquinating enzymes, certain kinases and proteases --- are "`regulated"' by being brought to one or another of many potential substrates by auxiliary docking proteins (e.g. transcriptional activators). these regulatory interactions require interactions between simple adhesive (but specific) surfaces. this kind of regulation is highly `evolvable' : new and expanded meanings to signals are readily generated by simple changes in protein surfaces.  mark ptashne
the flux-corrected transport algorithm on the ncube hypercube  this work describes the implementation of a finite-difference algorithm, incorporating the flux-corrected transport technique, on the ncube hypercube. the algorithm is used to study two-dimensional, convectively-dominated fluid flows, and as a sample problem the onset and growth of the kelvin-helmholtz instability is investigated. timing results are presented for a number of different sized problems on hypercubes of dimension up to 9. these results are interpreted by means of a simple performance model. the extension of the algorithm to the three-dimensional case is also discussed.  d. w. walker g. c. fox g. r. montry
hypercube performance for 2-d seismic finite-difference modeling  wave-equation seismic modeling in two space dimensions is computationally intensive, often requiring hours of supercomputer cpu time to run typical geological models with 500 × 500 grids and 100 sources. this paper analyzes the performance of acous2d, an explicit 4th-order finite- difference program, on intel's 16-processor vector hypercube computer. the conversion of the sequential version of acous2d to run on hypercube was straightforward, but time-consuming. the key consideration for optimal efficiency is load balancing. on a fairly typical geologic model, the 16-processor intel vector hypercube computer ran acous2d at 1/3 the speed of a cray-1s.  l. j. baker
rna biology and the genome (abstract only)  the sequence of vertebrate genome is expressed by rna splicing producing mrna. interpreting the genome requires understanding the sequences recognized by the nuclear factors and spliceosomia executing removal of introns. the status of this area of science will be reviewed. conversely, genome sequences can be searched for sequences which specify rna splicing and are common of many genes. the availability of genome sequences from a variety of species will make the latter approach much more powerful. the recently discovered rna interference (rnai) process is evolutionarily old and related processes are important for control of expression of repetitive genes in some organisms. rnai can be initiated by conversion of double strand rna into 21-23 nucleotide rnas which can base pair with mrnas and direct their cleavage. these short rnas may also direct silencing of genes by other mechanisms. over half of the genome of many organisms is composed of repetitive sequences and it is possible that rnai may silence these sequences.  philip sharp
towards predicting coiled-coil protein interactions  protein-protein interactions play a central role in many cellular functions, and as whole- genome data accumulates, computational methods for predicting these interactions become increasingly important. computational methods have already proven to be a useful first step for rapid genome-wide identification of putative protein structure and function, but research on the problem of computationally determining biologically relevant partners for given protein sequences is just beginning. in this paper, we approach the problem of predicting protein-protein interactions by focusing on the 2- stranded coiled- coil motif. we introduce a computational method for predicting coiled-coil protein interactions, and give a novel framework that is able to use both genomic sequence data and experimental data in making these predictions. cross-validation tests show that the method is able to predict many aspects of protein-protein interactions mediated by the coiled-coil motif, and suggest that this methodology can be used as the basis for genome-wide prediction of coiled-coil protein interactions.  mona singh peter s. kim
a perspective view of the modcon system  in this paper, a system of computer programs for the geometric description of hot forgings is outlined. the system is known as the modcon system which stands for modular construction. the modcon system allows quite complex forging shapes to be produced from relatively few input instructions. the forging geometry is defined as a series of volumetric modules which are then merged together during generation of the n.c. tape necessary to machine the finishing-cut edm electrode for the whole forging cavity. the system can also be used for the roughing cut of the edm electrode before the finishing cut stage as well as for generating cross-sectional data which serves as input to subsequent preform design systems. the system represents a considerable saving in time and cost over current methods involving conventional pattern making for the copy milling of electrodes.  y. k. chan