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Comments · 479

  1. Re:Why just Perl? on Bioinformatics · · Score: 2
    While Perl is great for cranking out some web sites with high mutation rates anyway, IMHO Perl is a maintenance nightmare.

    Anyone tried to do non trivial changes to his old Perl programms?

    My Perl programs were those that were the hardest to get understood after I had stopped working with them for some weeks. It is usually easier to rewrite them.

    Nonetheless I valued the good performance of Perl programs and was thus sceptical to other kids on the scripting language block, like Python.

    Months later, I must say that the much saner syntax of Python, the formidable documentation and the large library have changed my scripting preference from Perl to Python. Like Perl, Python has been ported to a lot of platforms.

    Ruby is a language I have not looked into yet. Its strong Japanese supporter base, has led to a lot of FreeBSD ports. So I might have a look soon.

    BTW, there are bioperl, biopython, bioruby and biojava efforts - anyone spotted a bioc or bioc++ one? And some dork registered www.biofortran.org.

  2. Re:Twenty Points To Whomever Finds DeCSS in DNA on Bioinformatics · · Score: 2
    I wonder what the odds are of finding one of these sequences in the billions of combinations currently being sequenced?

    But what is your reference DNA?

    There are regions on the chromosomes that are common to all individuals (like sequences that encode important cell machinery), while there are regions that vary more or less among indiviudals (e.g. those couple of nucleotides that differ between George Bush jr. and Al Gore :)

    And of course with ongoing research some of the DNA map data gets rewritten with higher accurate data versions (as it has been happened with the geographical world map in the past).

  3. Re:Applying Open Source philosophy to Bioinformati on Bioinformatics · · Score: 2
    In addition the skills requirements usually include advanced degrees in biology or statistics, things few average programmers can offer.

    There are a lot of open source bioinformatics projects. These are typically spawned by university or other public research projects. You mention Python and Perl, so try bioperl or biopyhon for a start.

    The one thing I didn't like about the biotech industry was how their research and information distribution was tied closely to their purse strings.

    You will have a lot of open source (where the majority of development money will come from public research funds) and a lot of commercial applications.

    It is unlikely that a large bunch of hackers will revolutionize this field. This is because you need a lot of domain specific knowledge and because a lot of work that needs to be done is too tedious or uncool to attract open source people from outside the bioinformatics field.

    Something like the Gimp could be done, because nearly everyone needs such a tool - but who needs for example a multiple sequence alignment editor besides biologists?

    Did you see some open source satelite control software or hydrodynamic simulation from outside their engineers communities?

  4. Re:Bioinformatics on Bioinformatics · · Score: 2
    Some words in advance:

    I worked for a company in cheminformatics so to say, we did software to gather and evaluate spectral and structural data, to store and retrieve it from a large database. Then I went to company that developed software for banks. Today I work in a bioinformatics company.

    The scenario was roughly the same, a lot of data in one or various databases, plus software to browse and manipulate that data. The difference is probably in the scale, the sheer amount of data, which is huge in bioinformatics.

    Compared to the guys from the financial software, the physical chemists had to work really hard!

    The problems were advanced and the number of customers, large chemical companies was less than the number of financial instutes in the second company.

    I believe the same will hold for the bioinformatics. What I can't tell however are the margins. The bankers seem to had a much better profit margin than the physical chemists. No idea what the bioinformatics customers are willing to pay. I expect pharmaceutical companies to be able to spend more on their tools and services than general chemistry companies.

    On the other hand, the present bioinformatics hype will probably to lead to a lot of competition.

    So I am not sure what will happen. Could be a good market, could be a very tough market. What I am sure of however is that the job is very interesting. State of the art software development, state of the art scientific work.

    In addition the skills requirements usually include advanced degrees in biology or statistics, things few average programmers can offer.

    Yes and no. You need a diverse team of specialists. Of course you will have scientists there, some molecular biologists, and experts in genetics, perhaps some mathematicians or computer scientists. But because you need to create good software as well, you need very good software people. Good database people, good GUI programmers, good software architects etc. Even good system admins for the large machines.

    So people need to be specialists in their IT subject plus be able to work in the bioinformatics domain as well. Interesting for me to see that many physicists seem to have this profile.

  5. Re:Now, to get AMD to admit BSD exists. on FreeBSD/Alpha SMP fully multiuser stable and checked in · · Score: 3
    I build and run FreeBSD-CURRENT for years on AMD boxes (at present K7-700 at work and K6-300 at home) and had no processor problems at all.

    My guess is that your motherboard is either bad quality, or perhaps needing a decent BIOS update. Another candidate could be your RAM. I once had problems with an old Asus SC-200 SCSI controller, that was not up to the task with faster systems anymore. Overclocking is a bad idea as well.

  6. Re:No experience on How Does One Become a Game Designer? · · Score: 1
    Get Cygwin. They finally manged to have package update system over the internet.

    The gcc is able to bind against the MS libc, if you want (Mingwin).

    But for a real project, people will use MS devstudio.

  7. Re:just dive in! on How Does One Become a Game Designer? · · Score: 2

    Okay, perhaps they are too old, but the doom and quake engines are available for free on the net. Plus the black book from Michael Abrash is online over at Dr. Dobb's. It describes the techniques behind doom. Even in the times of Direct X and Open GL there should be some wisdom in it.

  8. mostly self educated, pragmatic problem solvers on How Does One Become a Game Designer? · · Score: 3
    Two of my colleagues came from a game company. One of them working as a lead programmer on a recent top ten title.

    Of course we talked about their prior job in game industry - doing a killer game is a dream many programmers have.

    From what they told me, it is a very tough business. People seem typically to start young, with no prior education, being recruited from the amateur scene. Job hours are long, payment is low. And of course one needs to stay on the frontier of the hard and software.

    Assembly programming is done by few specialists (like game engine designers), C/C++ is the implementation language, with software design techniques just starting to get introduced.

    From comparision to the people I knew from the scientific and economic scene, these guys are fast pragmatic programmers, not so much on the theoretical side (the feared property of CS graduates :) Possibly that fast problem solving capability is the key feature to survive in the hard gaming industry. I was surprised to hear what simple tricks are sometimes used - just to get the deadline.

  9. Template Meta Programming on Open Source Programming Language Design · · Score: 2
    Wow, the coolest hacking link I saw on Slashdot for a long time!

    I always knew that C++ offers more ways for obfuscated programming than C - I can't wait to show these snippets to my colleagues. :)

    And funny to realize that I have just bought the book on Generative Programming that has been mentioned on that template meta programming page that features the Meta Lisp for C++ interpreter.

    One more reason to read the book soon.

    Mod this up!

  10. Donald E. Knuth's real reason for TeX on Will There Be Historical Records from the Digital Age? · · Score: 2
    I have posted it in several discussions on Slashdot, that Donald E. Knuth's TeX typesetting system was not only intended to create high quality typeset mathematics, but that Knuth's deeper reason was to preserve his work in a high quality format for the ages to come.

    This is no coincidence, because Knuth's main oeuvre, a several volume work on computer science, has already a related aspect:

    Computer science changes very fast and Knuth decided to include just those parts of computer science that have settled and that might have reached a maturity that would make them unlikely to get radically changed in the future. Hard task. And indeed that stuff he put into his three released volumes is highly mathematical, because such stuff is typically evolved enough, but still he did not really manage it, so the RISC architecture for example pushed him to update his machine language MIX.

    At some point, when Knuth got some copies of his TAOCP, he was frustrated enough because of the typographic quality getting worse. So he decided to take some time off to develop a system that turned out into TeX (who else than a professor can take 10 years sabattical to do such :-)

    To shorten the story:

    Knuth developped TeX, the programm that assembles boxes into lines, lines into pages, pages into documents. Developped Metafont, the programm that takes the mathematical description of font families (= a meta font) and renders them into bitmaps. He developped the computer modern fonts in Metafont format. Plus he invented a system called literate programming, that allowed to derive programming code and documentation from the sources.

    All this, has been released in form of five books:

    • TeX manual
    • literate/commented TeX source
    • Metafont manual
    • literate/commented Metafont source
    • literate/commented Computer Modern font sources

    This means, that even in hundered of years, everyone with those 5 books, something like a computer, and the ability to read mathematical texts plus the computer science knowledge to implement a Pascal like language, will be able to reconstructs Knuth's whole system!!!

    If at that point .tex sources are available (at least as printed listings!), they will be able to hack device drivers for their then common output devices and to be able to print all of Knuths works in original typographical quality!

    That is real deep reason for Knuth's TeX - longevity of information.

  11. London? Paris!! on William Gibson On Japan · · Score: 2
    Gibson should take a closer look on Paris before he praises London.

    The French share

    • the love for fish (there are great Japanese restaurants in Paris),
    • the love for fashion,
    • the love for graphical arts (guess who reintroduced anime and manga into Europe)
    • the love for fast modern trains

    Alas the sense of cleanliness is rather shared with the Swiss (Paris toilets? Yuck!).

  12. Re:Java, anyone? on Curl Instead of Java or JavaScript? · · Score: 2
    curl is competing with several entrenched technologies, and both Flash and Java Applets have progressed a great deal over the last couple of years

    Flash looks nice and has been embraced by the web design community due to it allowing better graphics/layout than all those cranky HTML/Java solutions and good tools for non programmers beeing available.

    But its download time is a bad joke. It has spawned a sub genre of "loading"-flics, not unsimiliar to the pre-film fill material of older cinema days.

    Its seems to run reasonably well on its few supported plattforms. (Except for the Netscape 6 desaster)

    Java could have been very promising on the graphical side (look for example over there at John Maeda's applets ) but it is also a PITA regarding download times (SWING, Baby!).

    Plus Java's mutation rate has degraded the easiness of embodying an applet with a simple APPLET tag into a nightmare of version mismatchs between applets and browsers/VMs and forces users into using a Sun tool to construct a proper sh*tload of JavaScript that figures on what browser it sits and pulls in a proper Java VM in case the browser is too old.

    On the other hand who would not forgive Netscape to give up the internal VM and stick that cr*p into an external plugin, if the internal VM was guilty of a big lot of bugs. (Run once, debug anywhere)

    And of course has anyone written a Java tool suited for those non programmers that web designers are yet?

    Thus Flash is partly useful to the artists and Java partly useful to the hackers.

    If curl is useful to both it will have a chance on the web. It seems to address graphical expressiveness (and more than managing a fixed rectangle in the browser), intelligent downloading strategies, obligations as programming language, obligations for non programmers (providing authoring tools).

    Its lack of cross plattfrom right now however is very bad.

    I also have no clue, if any open implementation will be possible.

  13. Re:Easy answer: on Why Isn't BSD a Desktop Operating System? · · Score: 2

    There are 2D drivers of course, and a driver for XFree86 3.3.x series that has been used by the Utah glx project. This Utah glx driver is better than nothing (I fact I used to play Quake with it), but much slower than the binary driver release for XFree86 4.0.x series.

  14. Re:SOAP parody on TCP/IP Over HTTP · · Score: 2

    Me thinks you're completely right.

  15. Re:Who invented what? on History and Culture of Computing? · · Score: 2
    For a development so recent, there is considerable controvery over some basic details. For instance, consider GUI. Popular folklore attributes it to Parc, followed by Apple.

    It is even not sure who invented the Macintosh, perhaps it was Jef Raskin perhaps some others (even Jobs) had a good idea or two during its development too.

    It's amazing that with all the people involved in these inventions still alive today, nobody quite agrees on who invented what.

    Jef Raskin is certainly not amused. While I can't judge if he was the true father of the mac, his saying that the truth was far less sexy than the common myth (he a former professor in contrast to some dropped out students) seems reasonable to me. Raskin had the necessary background, and it is more probable to me that the mac was no accident but the result of a longer line of thought.

    It's another matter trying to figure out who invented the first computer.

    Sure, Konrad Zuse together with his Plankalkül language.

    By the way - that teacher has to tell, that one of the first higher languages, COBOL, was invented by a woman, Admiral Grace Hopper.

  16. Re:Put it in a museum on Michael Abrash's Black Book For Download · · Score: 1
    Definately worth a good read, along with his 'Zen of Code Optimization'.

    Hm, I have to have a look at my copy of the Black Book, I think he put the "Zen" on the Black Book's CD-ROM.

    In that case, the online version would be less rich regarding information than the print copy. :-)

  17. Re:headline trolling on All Science is Computer Science [Y/N]? · · Score: 1
    Ahh, but all science _IS_ quantum physics, in that if you apply the rules of QM to your system, it will give the correct answer.

    Please apply those ideas to gravity. :-)

    Fun aside, unless someone comes up with the GUT, putting together the particle/field ideas from the quantumn theories of electro-weak and strong interaction with the geometric ideas from general relativity, I have serious doubts that quantumn mechanics (which one? :-) covers all of science.

    As for math on the other hand, it is true that nearly all science involves math, but if you just go by the math equations, you can sometimes get non-physical solutions.

    Of course. Mathematics provides a lot of consistent models (heck even a lot of consistent mathematics depending on how you choose the axioms), but picking that model that modells reality is physics.

    On a side note it is rather interesting how many professors of theoretic computer science seem not to care much about quantumn computing.

    The basic models from the theory of computation on which various famous theorems rely (including the halting problem) all stem on a model that models a machine governed by the laws of classical mechanics, which is only a approximation of course, as nature is mostly quantumn mechnical. Thus computation models that model a quantumn mechanical machine are supposed to show different computational behaviour.

    When talking about such systems, the usual computer scientist gives you a look like you were talking about warp drives.

  18. Re:nitpick on Guido Von Rossum on Python · · Score: 1
    My surname is Van Der Vliet and always has been. Not sure why the family capitalises the V & the D though, which is technically incorrect.

    It is common practice in Dutch news papers, to captialize those middle names if they stand alone without first names.

    Those Germans who have a van in their name, like Ludwig van Beethoven are simply of Dutch origin, the countries are neighbours after all. And consider that probably 700-800 years ago, they were not seperated but part of the same reich, the languages at that point very close together (you can still hear common bits to Dutch, German dialects and Swiss German dialects).

    In both German and Dutch case, the von or van does not clearly indicate nobility, both commons and nobles carry it. Example is actress Audrey Hepburn, her mother was a Dutch baroness van Heemstra. But in case of Germany, the majority of the von carriers have some noble origin, and in the Netherlands, an even larger majority of the van carriers are common. Thus the different conception.

    Ah it is great to start a day this silly. :-)

  19. Re:What a TERRIFIC idea! on Linux On Windows - The Thin End Of The Wedge? · · Score: 1
    Considering that XFree86 has been supported on OS/2 for many years, I would hope that a Windows version is not beyond the realm of possiblity.

    In case of OS/2 it was Dr. Holger Veit, a talented programmer, with time on his hands (working in an academic public founded society) that sunk his teeth into the port.

    Perhaps present Cygwin people have less time or talent available right now.

    There is of couse no technical impossibility here.

  20. Re:What a TERRIFIC idea! on Linux On Windows - The Thin End Of The Wedge? · · Score: 1
    According to the Cygwin project , XFree86 4.0 already compiles and runs under cygwin without patching, and has for some time.

    Uhm, at some points you could compile all af XFree86 4 under Cygwin, but last time I tried it, compilation of the Xservers was not possible.

    I was very surprised to learn this a few weeks ago; I would think many people would have the same excited reaction, but it's not a well-publicized part of the Cygwin project.

    This probably is because the Cygwin team that strives for XFree86 compilation has not managed to keep the tree working on their platform most of the time.

    I consider XFree86 compilation under Cygwin highly experimental at this time.

    What excited me more the last time I checked Cygwin was them having set up a simple but sufficient way to distribute packages. It is quite easy to update that package collection via the internet and thus fetch the latest stable and experimental packages for Cygwin. This is a big leap forward.

    Should XFree86 become stable for Cygwin, I expect them to put it in that distribution system as well.

  21. Reason behind Knuth's TeX on Rebooting The World? · · Score: 2
    By now they also have problems with the multitude of different text formats (WP 5.1 anyone?).

    To ensure value over a long period was actually the motivation behind both Donald E. Knuth's books on computer science (he put in only that stuff that seemed to him have reached seminal status, that would matter in a couple of decades or centuries, like a lot of mathematics does) and his 10year off holiday to create the TeX typesetting system:

    Knuth was frustrated, that in a period where mathematical texts were typeset in a crude way, the typographical quality of his books degraded more and more. So he created one of the early digital typesetting systems, using one of the early laser printers (hm, I should reread that one from Knuth's excellent documentation "Digital Typography", that is a making-of-TeX :-)

    So he got into the art of typsetting, created a program for putting font descriptions (meta fonts) into rendered bitmaps (Metafont), wrote those descriptions (Computer Modern font), wrote a program that could put boxed characters into lines, lines into paragraphs, paragraphs into pages (TeX).

    Even more interesting he did his programming in a way, where he could generate source code and documentation from one common source, something he called literate programming (web/tangle) - a system that put javadoc to shame.

    That documentation is actually a very good commented version of the source.

    So the end result were two volumes with text books that explain the use of the TeX typesetting and the Metafont font generation software, two volumes that list the TeX and Metafont sources (with lot of comments), and the volume, that lists the font descriptions.

    This means, that using these five volumes, that are thought to be kept around a longer time as real books, plus the knowledge of some higher mathematics and computer science (like a pascal definition and some books on programming) would suffice some halfways decent gifted individual in the far future to recreate a simple pascal like programming language, and then bootstrap the whole Knuth TeX system (down to the fonts) from the knowledge and listings in the five Knuth books. If you then have some *.tex sources around, you could compile them on your then existing computer and print them on your then existing printer.

    I want to stress this, because most people think TeX is just some crude high quality math typesetter. No it is about being able to reproduce high quality maths in the far future.

    For truly longish messages into the future (like pyramides or nuclear waste or climate change), I recommend a book by renowned hard scifi writer Gregory Benford about that matter.

  22. Re:Improving crossplattform C/C++ graphics libs on Carmack on D3 on Linux, and 3D Cards · · Score: 1

    Sorry, Havoc's lib is called Inti.

  23. Improving crossplattform C/C++ graphics libs on Carmack on D3 on Linux, and 3D Cards · · Score: 1
    Does anyone have any ideas what development tools could be used to help cross platform development? Of course, I'm not suggesting some Java applet blazing at 1 mph,

    Ah, your putting salt in an open wound of mine..

    Bloody truth is, that the Java2D API is pretty much more advanced than what QT or GTK+ offer in the 2d realm right now. Java3D does not look unpromising too. And indeed Moore's law and stuff like HotSpot helps JAVA a lot.

    The question is how to improve matters?

    QT is nice, but probably not too open for external patches and not available as free software for the important Win32 platform.

    GTK+ is done by a group of people, I could relate most with, but it is C based and not C++ from the ground up. I'm not really sure how much Havoc Pennington's Incal layer will improve things (don't come with GTK--).

    The third option of writing a new lib from scratch is an enormous task. (Think mozilla what happens to people who reinvent a wheel)

    Plus it seems clear to me that more realism, use of rendering techniques (like what Apple used with Aqua - 128pixel icons, use of alpha channel) is the way to go. And I don't see that with either QT or GTK+ right now.

    I wish I had more time. Ah probably I am stupid enough to try ..

  24. Re:Welcome Ogg...you're a little late on Ogg Vorbis Changes (Just About) Everything · · Score: 1

    What is the Schmidt-Hefelman (or Heffelman) procedure about? Do you have any reference?

  25. Re:GPL Legal then? on Balancing Third Party "Ownership" Against The GPL? · · Score: 2
    If your superiors either in the contract agency or the military agreed to let you use the GPL, without them understanding what that meant, chances are their permission is arguably invalid.

    Uhm? Who actually understands the GPL in its full glory, it actually having been never fought in court.

    Under that reasoning, a LOT of people could retract their GPL licensing.. :-)