Pub Date : 2003-09-01DOI: 10.1109/MCISE.2003.1225866
J. Rundle
Self-organized criticality in earth systems reviews recent research that applies a variety of statistical and statistical mechanical techniques to current problems of interest in the earth sciences. The topics it covers are similar in many respects to Donald L. Turcotte's now-classic work fractals and chaos in geology and geophysics (first published by Cambridge university press, 1992), and more recently updated (Cambridge university press, 1997).
地球系统中的自组织临界性回顾了最近应用各种统计和统计力学技术来解决当前地球科学中感兴趣的问题的研究。它涵盖的主题在许多方面与唐纳德·l·特科特(Donald L. Turcotte)现在的经典著作《地质学和地球物理学中的分形和混沌》(由剑桥大学出版社首次出版，1992年)相似，最近更新(剑桥大学出版社，1997年)。
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The punchline of this message is that computation changes everything, high-speed computation changes everything quickly, and lots of people doing lots of high-speed computation changes everything a lot.
这条信息的要点是计算改变了一切，高速计算很快改变了一切，很多人做很多高速计算，一切都改变了很多。
{"title":"From the Editors: Reproduced and Reproducible Results","authors":"F. Sullivan","doi":"10.1109/MCSE.2003.10005","DOIUrl":"https://doi.org/10.1109/MCSE.2003.10005","url":null,"abstract":"The punchline of this message is that computation changes everything, high-speed computation changes everything quickly, and lots of people doing lots of high-speed computation changes everything a lot.","PeriodicalId":100659,"journal":{"name":"IMPACT of Computing in Science and Engineering","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2003-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76775439","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
the ones I took as an undergraduate a few decades ago. (Digression: it’s time to start computing dates in “Jack Benny time units.” In such units, my courses were a few months ago.) Several things about these courses struck me as worthy of note. At first glance, some of the topics in the chemistry courses looked to me like the ones I’d had in physics courses. But I checked my old textbooks and found that I was wrong. The basic notions of quantum theory and statistical mechanics have been part of the undergraduate chemistry curriculum for a long time. Once I’d started rummaging through old texts, it was hard to stop. That’s why it’s important not to look at anything when trying to clear out old files and papers. If you look at it, it becomes a treasure. Anyhow, I began to notice other things about my old textbooks. Modern books are bigger—much bigger—than older ones. Observation of many bright summer interns tells me that this is not because students used to be smarter. I suspect that current technology creates the opportunity for including lots of fancy and informative graphics at moderate cost. There’s also the fear of leaving out something important. To see this at work, just try plotting the number of pages of some well-known text as a function of number of new editions of that text. A more important change is that lots of topics that were once considered “advanced” have migrated into “elementary” texts. While I believe that we really do learn everything important when we’re very, very young, I doubt that this is the reason for the change. As time goes on, and new subjects are understood better, they simply seem to become more, well, simple. The most important thing I noticed is that, in some sense at least, chemistry really has become physics, and so have some branches of biology. To put it more accurately, subjects that used to be thought of as separate and distinct are merging. And the place where they meet is in computation. All three subjects—physics, chemistry, and biology—are now deeply dependent on computation as their principal research tool, as are many other research subjects. The theme articles in this issue of CiSE contain several very good illustrations of this fact for the case of computational chemistry. Other theme issues have given other illustrations. Computational science has become the universal language of all other sciences. But what is computational science itself? Naturally, I can’t answer this question. However, thinking about it and trying to formulate at least part of the answer is a good task for everyone in the field. In my opinion, the definition of computational science is tied up with the description of how to train someone to be a computational scientist. If we know what constitutes education in a subject, we must have at least some idea of what the subject is. Many universities are now starting programs in computational science. CiSE will certainly be one forum for discussion of these programs, and some of the
{"title":"Computational Science: We'll Know It When We See It","authors":"F. Sullivan","doi":"10.1109/MCSE.2003.10004","DOIUrl":"https://doi.org/10.1109/MCSE.2003.10004","url":null,"abstract":"the ones I took as an undergraduate a few decades ago. (Digression: it’s time to start computing dates in “Jack Benny time units.” In such units, my courses were a few months ago.) Several things about these courses struck me as worthy of note. At first glance, some of the topics in the chemistry courses looked to me like the ones I’d had in physics courses. But I checked my old textbooks and found that I was wrong. The basic notions of quantum theory and statistical mechanics have been part of the undergraduate chemistry curriculum for a long time. Once I’d started rummaging through old texts, it was hard to stop. That’s why it’s important not to look at anything when trying to clear out old files and papers. If you look at it, it becomes a treasure. Anyhow, I began to notice other things about my old textbooks. Modern books are bigger—much bigger—than older ones. Observation of many bright summer interns tells me that this is not because students used to be smarter. I suspect that current technology creates the opportunity for including lots of fancy and informative graphics at moderate cost. There’s also the fear of leaving out something important. To see this at work, just try plotting the number of pages of some well-known text as a function of number of new editions of that text. A more important change is that lots of topics that were once considered “advanced” have migrated into “elementary” texts. While I believe that we really do learn everything important when we’re very, very young, I doubt that this is the reason for the change. As time goes on, and new subjects are understood better, they simply seem to become more, well, simple. The most important thing I noticed is that, in some sense at least, chemistry really has become physics, and so have some branches of biology. To put it more accurately, subjects that used to be thought of as separate and distinct are merging. And the place where they meet is in computation. All three subjects—physics, chemistry, and biology—are now deeply dependent on computation as their principal research tool, as are many other research subjects. The theme articles in this issue of CiSE contain several very good illustrations of this fact for the case of computational chemistry. Other theme issues have given other illustrations. Computational science has become the universal language of all other sciences. But what is computational science itself? Naturally, I can’t answer this question. However, thinking about it and trying to formulate at least part of the answer is a good task for everyone in the field. In my opinion, the definition of computational science is tied up with the description of how to train someone to be a computational scientist. If we know what constitutes education in a subject, we must have at least some idea of what the subject is. Many universities are now starting programs in computational science. CiSE will certainly be one forum for discussion of these programs, and some of the","PeriodicalId":100659,"journal":{"name":"IMPACT of Computing in Science and Engineering","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2003-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73920522","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2003-05-01DOI: 10.1109/MCISE.2003.1196303
C. Buchen-Osmond
The International Committee on Taxonomy of Viruses database is a universally available taxonomic research tool for understanding relationships among all viruses. ICTVdB's fundamental goals are to provide researchers with precise virus identification and to link the agreed taxonomy to sequence databases.
{"title":"The universal virus database ICTVdB","authors":"C. Buchen-Osmond","doi":"10.1109/MCISE.2003.1196303","DOIUrl":"https://doi.org/10.1109/MCISE.2003.1196303","url":null,"abstract":"The International Committee on Taxonomy of Viruses database is a universally available taxonomic research tool for understanding relationships among all viruses. ICTVdB's fundamental goals are to provide researchers with precise virus identification and to link the agreed taxonomy to sequence databases.","PeriodicalId":100659,"journal":{"name":"IMPACT of Computing in Science and Engineering","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2003-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83102539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Do you believe in your software's output? How much do you trust it? These questions force us to think about computation in a different and important way. In fact, understanding how much to trust the results is as important as the results themselves. Here are four different "degrees of belief" that i might have for results of my own computations, depending on the purpose and kind of calculation.
{"title":"How Right You Are","authors":"F. Sullivan","doi":"10.1109/MCSE.2003.10003","DOIUrl":"https://doi.org/10.1109/MCSE.2003.10003","url":null,"abstract":"Do you believe in your software's output? How much do you trust it? These questions force us to think about computation in a different and important way. In fact, understanding how much to trust the results is as important as the results themselves. Here are four different \"degrees of belief\" that i might have for results of my own computations, depending on the purpose and kind of calculation.","PeriodicalId":100659,"journal":{"name":"IMPACT of Computing in Science and Engineering","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2003-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83917330","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2003-03-25DOI: 10.1109/MCISE.2003.1182967
B. Boghosian
"The Lattice Boltzmann Equation: For Fluid Dynamics and Beyond", by Sauro SucciOxford University Press, New York, 2001, ISBN: 0198503989, US$100During the past 10 years, a new class of algorithms based on the lattice Loltzmann equation (LBE) has been developed for computational fluid dynamics (CFD). These novel and fascinating algorithms were inspired by kinetic theory a branch of statistical physics. They defy the conventional wisdom of CFD in that they provide stable, fully explicit differencing schemes, with no need for elliptic solvers or upwind differencing. Yet, they are also remarkably simple. In fact, the typical reaction of long-time CFDpractitioners when encountering lattice Boltzmann algorithms for the .rst time is often something like, "that can't possibly work. It's too easy."
{"title":"A Look at Lattice Boltzmann Equations: The Lattice Boltzmann Equation: For Fluid Dynamics and Beyond","authors":"B. Boghosian","doi":"10.1109/MCISE.2003.1182967","DOIUrl":"https://doi.org/10.1109/MCISE.2003.1182967","url":null,"abstract":"\"The Lattice Boltzmann Equation: For Fluid Dynamics and Beyond\", by Sauro SucciOxford University Press, New York, 2001, ISBN: 0198503989, US$100During the past 10 years, a new class of algorithms based on the lattice Loltzmann equation (LBE) has been developed for computational fluid dynamics (CFD). These novel and fascinating algorithms were inspired by kinetic theory a branch of statistical physics. They defy the conventional wisdom of CFD in that they provide stable, fully explicit differencing schemes, with no need for elliptic solvers or upwind differencing. Yet, they are also remarkably simple. In fact, the typical reaction of long-time CFDpractitioners when encountering lattice Boltzmann algorithms for the .rst time is often something like, \"that can't possibly work. It's too easy.\"","PeriodicalId":100659,"journal":{"name":"IMPACT of Computing in Science and Engineering","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2003-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77334724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Literature in fact, all the arts are customarily in the middle of some "movement" that promises to change the whole nature of the endeavor. Recent movements include hyperrealism, symbolism, deconstructionism, existentialism, surrealism, and many other "isms." One interesting literary movement goes by the name of minimalism. In a minimalist work, sentences are short, as are paragraphs. Even minimalist books are short, with very little narrative connective tissue. Most of the story is told via dialogue, which in the best examples, tells the characters' hidden story and makes the reader care about what happens to them.
{"title":"From the Editors: Less Is More (Is Less)","authors":"F. Sullivan","doi":"10.1109/MCSE.2003.10002","DOIUrl":"https://doi.org/10.1109/MCSE.2003.10002","url":null,"abstract":"Literature in fact, all the arts are customarily in the middle of some \"movement\" that promises to change the whole nature of the endeavor. Recent movements include hyperrealism, symbolism, deconstructionism, existentialism, surrealism, and many other \"isms.\" One interesting literary movement goes by the name of minimalism. In a minimalist work, sentences are short, as are paragraphs. Even minimalist books are short, with very little narrative connective tissue. Most of the story is told via dialogue, which in the best examples, tells the characters' hidden story and makes the reader care about what happens to them.","PeriodicalId":100659,"journal":{"name":"IMPACT of Computing in Science and Engineering","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2003-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87197284","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
LIMS For several years I have been searching unsuccessfully for someone to review laboratory information management systems (LIMS) for this column. After looking into the subject myself, I can better appreciate why. The topic is so important and complex that books could be written about it; indeed , they have been. 1 Briefly, LIMS software helps laboratories schedule procedures , process and track samples and test results, collect analytical data, organize reports, and facilitate instrument checking and calibration. Modern LIMS can be enormous and almost impossible to review without a specific application in mind. Luckily, my correspondents tell me that a wealth of information is already available to prospective users. Instead of reviewing a particular vendor's offering as usual, I thus offer you a brief guide to more information on these essential systems. Originally developed in-house by individual analytical laboratories, customized solutions were eventually supplanted by commercial LIMS products developed by commercial instrument makers—primarily to get users for their own analytical tools. These systems often ran on minicom-puter controllers or mainframes, but general-purpose systems that ran on networked desktops and handheld entry stations that could be tailored to the needs of many users eventually became available. Two short summaries of LIMS development can be found online: Alan McLelland's " LIMS—Laboratory Toy or a Critical IT Component? " (Management System " (www.umsl.edu/~sauter/analysis/ LIMS_example.html). Modern LIMS products are extensive systems with linked databases that let researchers standardize data reporting methods and automatically collect data from instruments such as spectrometers and cromatographs. They also facilitate strengthened security by maintaining data validation, certification, audit trails, quality-control analysis, and record archiving. LIMS have become essential tools for many biological and chemical laboratories and manufacturing plants, as well as the pharmaceutical and petroleum industries and anyone else who needs to analyze and process massive amounts of test data. Because setting up a new LIMS can involve considerable reorganization of a firm's procedures, you should not underestimate the time necessary for installing the system and training employees. In fact, it is probably a good idea to involve representatives from each department from the start to ensure that no unpleasant surprises result during the changeover. Several firms provide third-party analyses of your needs for a laboratory management system. You can find them with a Google search for " LIMS evaluation. " Further information on this important topic is available at www.limsource.com, which features a large collection of resources, …
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{"title":"From the Editors: Frankenstein Jr.","authors":"F. Sullivan","doi":"10.1109/MCSE.2003.10001","DOIUrl":"https://doi.org/10.1109/MCSE.2003.10001","url":null,"abstract":"","PeriodicalId":100659,"journal":{"name":"IMPACT of Computing in Science and Engineering","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2003-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82560275","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Rarely do pundits focus on the law as a problem in America's response to terrorism. Indeed, both sides quickly claim that the law supports them, hence no change is necessary. The authors view this as too simplistic, and see legal interpretation as having real consequences on the War on Terror. They argue that the Courts should give deference to what the Executive Branch regards as the proper response to an emergency situation owing to its greater availability of information and resources to attack the problem, and the lack of information sources and skill in foreign policy that most judges possess. They argue against any stance other than deference and it is a tribute to their reasoning that they largely succeed in their efforts, with the exception of one convoluted chapter regarding coercive interrogation. How can one argue against an anti-terror policy based exclusively on the rule of law and constrained by due process? The authors do so by consulting the historical record and retrieving ideas from branches of social science. How the book justifies its views is perhaps more useful for readers than even the measures it advocates for the War on Terror. Going back to the Civil War, the authors repeatedly demonstrate that the Courts have tried to balance the security of the state against the rights of the accused. When the Taney Court tried to block Lincoln from rounding up southern sympathizers in Maryland, not only did Lincoln ignore the Court and suspend habeas corpus, but he later got the war-time Congress (free of southerners with Republicans in the majority) to legalize what he did. In short, when there is a palpable threat to the State that establishes the Courts, the Courts have tended to let the Executive Branch do what it says is necessary. The authors acknowledgehowever that this sliding scale alsomoves in the other directionwhen the palpable threat lessens, as in the cases that largely reversed the Smith Act after the Red Scare of the 1950s passed. Even duringwar time, defendants canmake a vigorous defense as in the Dilling case where Nazi sympathizers were prosecuted under the Smith Act during WWII and the defense “...objected to every act of the prosecutor and disputed every ruling of the judge...” (p. 239), and the case came to an end with the abrupt death of the exhausted judge and the dismissal of the case by the new judge. The first part of the book examines major theories of national security law and the chapters go by the titles of Panic Theory, Democratic Failure Theory, and Ratchet Theory, which by their names describe why the law reacts the way it does to national security threats. The last half of the book looks at applications of these theories to law such as Alternatives to Judicial Deference, Speech, Due Process and Political Trials, and Military Force, but the most interesting of these chapters is the one on Coercive Interrogation. However convincing the rest of the book is, the authors themselves seem to lack conviction
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