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Shipud writes "The National Science Foundation, Public Library of Science and the San Diego Supercomputing Center have partnered to set up what can best be described as a "YouTube for scientists", SciVee". Scientists can upload their research papers, accompanied by a video where they describe the work in the form of a short lecture, accompanied by a presentation. The formulaic, technical style of scientific writing, the heavy jargonization and the need for careful elaboration often renders reading papers a laborious effort. SciVee's creators hope that that the appeal of a video or audio explanation of paper will make it easier for others to more quickly grasp the concepts of a paper and make it more digestible both to colleagues and to the general public."

nazarijo (Jose Nazario) writes "As a biochemist by training, Jeff Augen's Bioinformatics in the Post-Genomic Era was very interesting to me. Though I left the field some years ago, I was using the bioinformatics tools that are covered in the book daily and still look in from time to time. Naturally I was curious to see a larger perspective, as well as any progressions, that have occurred in the past few years. Augen's book gave me part of the larger picture, but it could have done more." Read on for the rest of Nazario's review. Bioinformatics in the Post-Genomic Era author Jeff Augen pages 388 publisher Addison-Wesley Longman rating 7 reviewer Jose Nazario ISBN 0321173864 summary Genome, Transcriptome, Proteome, and Information-Based Medicine

Bioinformatics is the science of biological information, namely sequences and metadata about organisms and sequences. What's interesting about this field to many people, both in the sciences and outside of it, is the large volume of data that gets analyzed and the results that emerge on a daily basis. Obviously interesting for the medical advances and the rapidly growing business in the life sciences, there's a complex field that has developed in the past ten years or so. And following the sequencing of the human genome, new challenges have arisen for everyone involved. Augen's Bioinformatics provides a good introduction to this new field of research for students in the sciences, and anyone with a decent undergraduate education in modern biology. I think that this accessibility of the material is one of the book's biggest winning points.

After an introduction to the book and the subject area of bioinformatics (chapters 1 and 2), Augen begins at the level of the structure of a gene (chapter 3). Here, anyone with an undergraduate level understanding of genetics or molecular biology can begin using the book and bridging the gap to the new areas of modern bioinformatics. Augen then describes how basic sequence analysis is performed at the DNA sequence level (in chapter 4). The material in Bioinformatics covers some of the higher-level methods for sequence analysis, including hidden Markov models, neural networks, and pattern discovery, and introduces some of the common algorithms found to do this analysis.

Chapter 5 then covers transcription, the process of going from DNA to mRNA. Beginning with the biology behind this activity (the ribosome and the larger "transcriptome"), Bioinformatics then describes how you would perform transcriptional analysis. Here, Augen shows how you go from a wet lab to a computational lab and describes what classes of experiments you perform to gather data and then what kinds of analysis you perform on it. This chapter introduces some of the more common clustering techniques for data aggregation and understanding.

The next step in the DNA -> RNA -> protein chain is found in chapter 6, which covers the translation process. Coupled to chapter 7, which describes protein structure prediction and searching, these two chapters bridge the next gap between laboratory data and computational analysis. Protein folding and structure analysis was one of my pet areas of study as a graduate student, and Augen's text does a decent summarization of the field to date. The resources listed and techniques described are definitely on par with the common practices in the field.

Finally, Bioinformatics gets into the next major area of bioinformatics, medical databases. Augen's bridge from genetics to medical science is complete, and he discusses how medical professionals utilize databases and can begin to predict disease, for example, based on data mining. The final chapter, "New Themes in Bioinformatics," covers exactly that, but also what Augen refers to as "workflow computing," or basically going about being a bioinformatics scientist. One of my favorite emerging areas in bioinformatics, metabolic pathway elucidation, is also covered briefly.

I've shared this book with a few friends who are all studying computer science or practicing computer scientists. I did so because Augen's material does a good job of explaining my background and introducing them to some of the analysis forms I introduce into my own work. It does a good job of that, and gets them quite excited. Bioinformatics really bridges a number of fascinating areas of computer sciences, including data mining and high performance algorithms. Augen's Bioinformatics is a good introduction to the field for them, and really anyone who has studied a couple of biology courses in college.

Where the book falls short, however, can be grouped into two main areas. The first is the failure of Augen's presentation of the algorithms. While the methods used to describe computational algorithms in Bioinformatics is common for non-computer scientists, it's completely unusable for computer scientists who are used to a specific algorithm presentation style that looks more like pseudocode than rambling text. The ambiguities this presents for a technical reader are unfortunate, especially if anyone studying bioinformatics is supposed to be computer science literate. The book itself assumes a life science literacy, so this isn't an unreasonable expectation of the reader.

The second area that consistently falls short in the book is in the utility of the information given. While I am significantly happier with the quality and depth of material presented in Augen's book than in the O'Reilly bioinformatics series, where the book fails to deliver is in showing the reader how to actually use the data they gather. After all, the book shows various sequence analysis algorithms and discusses tools available to do this work, but it only devotes a few pages (out of over 370 in total) to a workflow that can be used. Also, the book fails to point the reader at very worthwhile web resources sometimes, including meta sites like the SDSC Biology Workbench site, and just says "some Perl scripts" for local data analysis. As such, you'll have to go a few extra miles on your own to make use of the data sources.

I guess a third complaint of the book for me is that Augen has ignored or omitted significant bodies of research that fit squarely into the scope of the book. For example, Ken Dill's research into protein folding models, as well as Martin Karplus' work on the subject, receives no mention, nor does the topic of Bayesian network analysis when Augen discusses time series data analysis. These aren't new, they've been around for many years and influenced most of the field, and their absence is noted. The book's spotty coverage in some places, like these, is noticeable.

Bioinformatics does a few things well, but overall reads too much like a biology textbook to be useful to the average computer scientist. More emphasis on the practice of bioinformatics and data analysis would have made this book stronger and complemented the substantive background material well. Finally, using an approach more similar to the computer science approach would have been a tremendous benefit, since the material really is computer science in part. That said, I think this is probably the best introduction to this exciting area of science that I have yet seen.

You can purchase Bioinformatics in the Post-Genomic Era from bn.com. Slashdot welcomes readers' book reviews -- to see your own review here, read the book review guidelines, then visit the submission page.

Licensed2Hack writes "The Cooperative Association for Internet Data Analysis (CAIDA), part of the San Diego Supercomputer Center at the University of California, San Diego has an analysis of the recent DDOS on SCO.com. Netcraft also has more information in their article and analysis graphs. Seems SCO was hit with a 50,000 packet-per-second SYN flood peak, which yields approximately 20 Mb/s each way, or about the capacity of a DS3 line."

dex writes "Tom Perrine and Devin Kowatch of the San Diego Supercomputer Center have issued "Teracrack: Password cracking using TeraFLOP and PetaByte Resources" (PDF, HTML version via Google). Using SDSC's prodigious computing facilities, they precomputed 207 billion crypt() hashes in 80 minutes."

dex writes "Tom Perrine and Devin Kowatch of the San Diego Supercomputer Center have issued "Teracrack: Password cracking using TeraFLOP and PetaByte Resources" (PDF, HTML version via Google). Using SDSC's prodigious computing facilities, they precomputed 207 billion crypt() hashes in 80 minutes."

tep-sdsc writes "Richard Morgan has a problem. His first novel, Altered Carbon, will be a tough act to follow. It is set in a future world that could rival Heinlein's Future History and Niven's Known Space. There's enough material here for a career, not just a (great) first novel." OK, so you know he likes it -- now read on for the rest of Tom's review. Altered Carbon author Richard Morgan pages 534 publisher Del Rey (US) rating Excellent reviewer Tom Perrine ISBN 0345457684 summary A future beyond death, through personality transplantation.

It would be easy to describe this book as "cyberpunk meets noir," but that would be a disservice to the reader, the author and the book.

Although this book is set in a future that is seems to be heavily influenced by the punk movement, with computers, hackers, weapons, and leather, this is no superficial, cartoon world setting for a quick romp through cyberspace. There is a depth and texture here that promises, and delivers, as a setting for a novel that could end up as influential as Vinge's True Names, or Stephenson's Snow Crash or Spillane's Mike Hammer.

The main technological trapping of this setting is the ability to digitize, store and transport human consciousness. Peoples' consciousnesses can, and are, digitized and loaded out of and into their bodies on a regular basis. The state uses this to punish criminals by storing their minds "in the stack" (digital prison) and the wealthy and powerful can have themselves "backed up" like yesterday's spreadsheets. Interstellar travel is via "digitized human freight." Human bodies ("sleeves") can be rented, bought and sold, to provide containers for these digitized minds. And this is just the background.

This is also a hardboiled detective thriller, easily the equal to Chandler or Hammett in both plot and characterization. There is a complex plot, the de rigueur dames and guns, but also some important themes that are surprising for the genre. The plot is never formulaic, with a depth and enough unexpected twists and turns to keep the reader guessing well into the last chapter.

The protagonist, Takeshi Kovacs, is no simple hardboiled detective; he's a cashiered UN "Envoy," qualified to do anything from holding a beach head or planning a military invasion, to taking over a government from within. People with this training are barred from public office and high government positions on most settled worlds. And Kovacs has been offered a job he can't refuse by one of the richest men in twenty planets: "Kovacs, find out who killed me."

On a deeper level, this novel asks some real hard questions, that get to the heart of what it means to be human. If you can digitize, back up and restore people, what is the meaning of death? Is the "soul" digitized, or just your memories? Does it matter? When bodies can be rented and exchanged, just what is "identity"? When people can buy new bodies and live for centuries, amassing power and wealth, how will that affect their humanity? Will they become more than human, or less? How will this effect human society? These issues are all raised subtly, this is no sermonizing sociology text masquerading as a novel.

But Morgan's novel remains at its heart a well-crafted detective story. No matter how corrupt the society, no matter how powerful the rich, in the end, justice comes from the smoking barrel of a hired gun, working for some fast cash, plus expenses. This books tries, and succeeds, on so many levels, that can only hope that this will be just the first novel from this new author. Somewhere, Chandler and Hammett are saying, "Ya' done good, kid. Now kiss the dame and get outta here."

(As I was finishing this review, I discovered that Morgan's second novel, Broken Angels, which continues Kovacs exploits, has just been published by Gollancz in the UK. I'll gladly pay international shipping to get my hands on this second book as soon as possible.)

You can purchase the Altered Carbon from bn.com. Slashdot welcomes readers' book reviews -- to see your own review here, read the book review guidelines, then visit the submission page.

Wee writes "I saw this morning that the San Diego Supercomputer Center has released Secure Syslog, a replacement for the standard Linux/UNIX syslog daemon they've been working on for some time. It adds security and performance features (modular design, highly scalable), while retaining backwards compatibility. According to their announcement, it is the first syslog implementation to target "syslog-reliable" (RFC 3195) functionality and it is the first syslog targeted at very high performance and forensically-sound auditing. It's currently under the UC's "free for non-commercial use" license, but they are looking at moving to a completely open license (BSD-style licensing was mentioned). If you have high-traffic systems and you need reliable syslogging, this might be a worth a look. Those needing syslogging over TCP/BEEP, sockets, etc as well as UDP might also want to check it out."

pluto378 writes: "SDSC has a report on their attempt to build a Terabyte fileserver for less than $5,000."

Random Walk writes "A group of researchers from the UCSD Supercomputer Center has used a technique they call "backscatter analysis" to study the prevalence and targets of DoS attacks. They claim that their study is "the only publically available data quantifying denial-of-service activity in the Internet", and provide interesting statistics on attack rates, durations, and victims." CT:This is an amazing report.

gle was one of many readers to write about an interesting security problem: "If you own an Alcatel DSL modem, you will be interrested to know that virtually anybody on the planet is probably able to reconfigure you modem, steal your passwords, sniff your data, install a custom firmware into it, or just break it for fun. Lack of proper authentification, and various back-doors have been pointed out amongst various design flaws. The man who discovered this is Tsutomu Shimomura, who got famous at getting Kevin Mitnick arrested. Alcatel claims 36% share of the DSL market, with more than 1.7 million units installed ..." So if you have DSL, you might want to check the label on the side of the modem about now.

MainFrame writes "A friend of a friend of mine, Tom Perrine, was "invited" to testify at the Congressional subcommittee meeting concerning Carnivore. "I had seen Carnivore on a recent trip to Quantico and had the opportunity to discuss the program with some of the developers. This was all before the Earthlink flap. I hope that my (written) testimony was balanced and fair. Those of you who know me, know that I try to balance my firm belief in personal privacy and Constitutional rights with my belief that there *are* times when law enforcement has legitimate needs and a duty to access electronic communications, when properly authorized by a court. " There's a lot of confusion about what carnivore is and what it does, so its nice to see something like this which appears to be much more informed.

Let's start this off with bio2's link to "the tube": an unrollable laptop:super crazy hardware. seizer sent us the most amusing firewall circumventer: a TCP/IP Email Tunnel. While on the subject of bizarre technology, John Petz sent us a webserver running on an Atari 800. Still not in shock? hool sent us a hack over at x42.com which uses the hostname as input to a calculator. tdunn linked us to a place that lists odd things found inside PC cases. It includes a *shudder* severed finger tip. For more wierd tech support, yeahbensteres submitted iamanidiot.com which has some tales that you may or may not believe. Pike sent us 94 Uses for Old Altoids Tins: Who eats 94 tins of altoids? Oh... wait. OwenF sent us linkage to the latest robotic pet craze. Look out AIBO, here comes Robotic Fish! Slashdot's own jamiemccarthy points us to TimeCube.com for all your wierd-science needs. You econ majors might be interested in Yhetti's link to the fortune-cookie market index. Bradley noted a story about a man who changed his name to 'Oxford University' to avoid domain squatting charges from Oxford University. If you have a mission:impossible scheduled next week, Dr. Manhattan sent us a link to a Swiss company that is developing self-destructing CDs. The CIA has some on back order. An anonymous reader pointed us to EarthKam, which has several really beautiful pictures of earth from space. Check out their top 10 ... if only they were bigger they'd make great background art. And finally for those of you who are sick of all the naughty language on TV, deepak saxena sent us a machine that claims it will filter all the damn swearing from TV and video. I'm waiting for a version that filters out Regis.