Unfortunately that means many people seeking easy course credits are going to be hit with a shock to the programming/maths skills as biology realigns to more complex techniques in shifting from wet to dry labs.
This sort of stuff makes me laugh. If only a computer was 1/10th as complicated as a cell. I find it is more the people trained in computer science who experience the shock when they come into a lab environment and see how complex, chaotic and large the biological data sets are that are routinely generated.
In my experience it is a rare computer scientist who can make the transition into bioinformatics and be truly effective, ie: not dependent on having a biologist sit with them 8 hours a day telling them what to do and why they're doing it, and can actually understand the breadth of the problem they're trying to solve, not just "develop a system to correctly pick these monoisotopic mass spectrometer peaks" or "build an algorithm to count the number of protein spots on a 2D gel"
It reminds me of a quote I saw published in a newspaper a while ago by an academic:
Biologists tend to write terrible computer code, but the computer scientists trivialise things and spend vast amounts of time solving problems that don't exist
Interesting what the author was saying about 2.2 versus 2.4 in terms of stability. We have 3 Linux machines which are used quite heavily here at the moment:
1) A dual PIII-800/Intel 440GX/512MB ECC RAM based server, with a Mylex AcceleRAID 170 adapter, an Adaptec AIC-7896 SCSI adapter, Intel EtherExpress Pro 10/100, and an external 450GB SCSI RAID-5. This box is used for NFS/Samba file serving and an e-mail server for around 100 users.
It runs kernel 2.2.17
2) A dual PIII-800/VIA 133 server/1GB PC-133 RAM server, with an Initio A100U2W SCSI adapter, Intel EtherExpress 10/100 and 70GB of external SCSI RAID 1/0. It runs MySQL, Apache, and a collection of internally developed Perl, C and Java server apps, on kernel 2.4.3
3) A dual PIII-450/Intel 440BX/512MB PC-100 RAM server, with an Adaptec 2940UW adapter, Intel EtherExpress 10/100 and 170GB of external SCSI RAID-5. It is used as a development system, and runs MySQL, Apache, and assorted Perl, C and Java apps, on kernel 2.4.1.
Systems 2 and 3 have both been up for 197 days as I type this, and would have been up for over 250 days had we not needed to power them down to move them to a new server room.
System 1 (with the 2.2.17 kernel) has never stayed up for more than 55 days. It hard crashes without anything informative being written to the logs, and obviously required the reset button to be pressed.
Has anyone got any ideas, given the hardware configs and software running on these machines why 2.2 is so horrendous, yet 2.4 so stable?
Then Sun decided to release their Ultra 5 workstations at 6k a piece or so, IIRC. The market for Solaris x86 went **POOF** in about 4 seconds. The damn things are real live UltraSparcs and they work like a hot damn.
Ouch. If your Ultra 5 worked like a hot damn I'd hate to see how slow your x86 Solaris boxes were. We have some of the original 270MHz Ultra 5s around here at work and they're disgusting to use. I haven't used one of the new Blade 100s yet, but I hope their IDE performance and graphics are better than the Ultra 5.
Anyone here used both an Ultra 5 and a Blade 100 for any length of time care to comment?
why not just move distributions over to dpkg/apt/DEB management like Debian, or FreeBSD-style ports
Riiiiigghht. And that will happen straight after Debian adopts the graphical Mandrake installer, which is completely superior to Debian's tired old offering. It's all free software, after all, isn't it?
bloated -- it comes with the kitchen-sink *AND* the kitchen-sink-devel RPMS installed by default, for Pete's sake
and that's the reason you wouldn't recommend it? what sort of admin does a default install of anything? are you installing a mail server? a file server? database? DNS? you've always gotta do some customisation, and when you do, mandrake is no more bloated than any of the other distros.
155 million rows here on a dual-processor IBM p620 with 2GB RAM and DB2 v7.2 and it screams along. get the right indexes and buffer pool settings and there's no problem.
We've just done exactly the same thing. I miss MySQL's overall simplicity...it makes it really easy to develop quickly. after 6 momths of using DB2, i still feel like it's more in the way than actually helping me get the app developed.
there's no way we can go back now either...we're an IBM strategic partner (but the upside of that is we get nice hardware to play with for free...where's the Regatta?)
Last I checked, every "l33t" hacker and his 10 year old friends consider AIX to be a "crappy" version of Unix.
I'm guessing your 'l33t' friends don't like a really rock solid journalling filesystem, a damn useful logical volume manager included in the base OS, support for logical hardware partitioning, scalability into the stratosphere, bundled Linux toolkit, and probably the most comprehensive GUI admin tool ever built.Why the hell would you want to run Linux on a machine like the p690?!?!
i will admit though that having to pay extra for an ANSI C/C++ compiler sucks...
On the other hand, it meant that most people who used OS/2 had a handle on right-clicking.
having to drag things around on the desktop with the right mouse button took a lot of getting used to as well...or am i remembering the workplace shell incorrectly?
except that a TV tuner card here in Australia costs under AUD$200, and a DV camera costs well over AUD$1500...in fact it may well end up costing more than the iMac.
The only other thing you'd want PCI for is for a second video card and that could be done through firewire if you really wanted
a video card running over FireWire? please...AGP was supposed to be a step up over PCI...going to less than 50% of the available bandwidth of PCI for a video card really isn't a step in the right direction.
Sure FireWire and USB can cover most bases...but even having one PCI slot would be an incredibly useful addition to the iMac, and wouldn't consume a lot of motherboard or case space.
Some posters here have mentioned that the fact that KOffice is free will be a significant factor in drawing people away from Microsoft Office. I'm not sure that's at all correct...A year or two ago, I remember seeing copies of Lotus SmartSuite 97/Milennium bundled with all sorts of PCs (not just IBM PCs), and OEM versions being advertised everywhere for AUD$30 (that's only about US $15).
SmartSuite 97 is probably still ahead of KOffice in terms of compatibility and features, plus it actually contained a famous component (Lotus 1-2-3), and it wasn't enough to stop it from sliding into complete obscurity.
KOffice (and StarOffice for that matter) have probably each got another 2 years or so of catching up before they even get close to where the now extict competitors of MS Office were a number of years ago...and being almost free didn't help them back then either.
And supposedly IBM will do this as well, along with making AIX "100% Linux compatible". Trouble is, I've been hearing this for years - and AIX still ships without a C compiler and behaves erratically when you try to install GCC, Perl, etc from anything other than pre-compiled binaries. And where is SMIT for Linux? I'm having a hard time finding evidence of IBM's billion dollar commitment.
that's exactly my experience too. can people here tell me...is it normal to waste days trying to compile stuff on AIX that compiles cleanly and without difficulty on Linux or Solaris? the Linux toolkit that comes bundled with AIX 5L is a little bit of help, but as the previous poster implied, stuff like gcc and bash doesn't really sit quite right with the rest of AIX, which can lead to some WeirdShit (tm) down the track when you're trying to compile supposedly 'standard' software.
Frankly, I'm still recommending 600 at max to most people.. The average user doesn't need 2 ghz to check their e-mail and such
You're not doing your friends any favours by recommending they get low-end machines. What happens when they decide they want to run their new copies of Windows XP and Office XP with all the bells and whistles and voice recognition turned on? Or use that Firewire port for something and start messing around with some funky video effects processing? Or play the latest flight-sim or FPS at full-res and maximum reality and physics? A fast CPU isn't everything, obviously, but it's sure as hell not going to hurt.
Software almost never gets faster, and consumer-type applications, like games and multimedia are some of the biggest CPU/graphics hogs outside of 'professional' level computung. I always recommend to friends to get the fastest machine they can afford. It might seem like overkill now, but you can bet in 12 to 24 months it won't be looking like an extravagance. Not everyone wants to run vi to edit C source code and marvel at how small and lean they can get their Linux kernel down to...
hmmm....the new Pocket PC OS is codenamed 'Merlin', and will contain speech recognition technology. that sounds exactly the same as OS/2 Warp v4.0. OS/2 lives! undoubtedly the Pocket PC OS 2003 edition will be based on CP/M, and feature floppy disk technology.
Linux combined with a TV...now there are even fewer excuses for the average lard-ass open source hacker to get outside and away from staring at a screen. Although...being able to watch an episode of Buffy while StarOffice starts up could be useful...
Absolutely! It's not so much that the average sysadmin is bad at their job, it's that they've got 50 machines to look after, and only enough time to realistically care for 10. Any products like this HP one which can make critical admin tasks like intrusion detection easier and more automated are worth every cent.
It's clear from the postings of a lot of people on this discussion to the effect of "your sysadmins must be all morons if they can't install snort and harden a linux distro themselves!!" that they've never had a sysadmin job in a big, busy company. It's simply not an efficient use of your time to be configuring and installing stuff like snort, or manually hardening a linux distro, when for $3000 you can have it all done for you, and backed by a company like HP.
Is it really worth to pay $3,000 for a distro with an Intrusion Detection System like snort [snort.org] configured ? I'd say the distro would pay for itself in about 2 seconds if it actually did what it is advertised to do. $3000 isn't much to pay to have HP say "This thing is guaranteed to be configured correctly, and work as advertised.
Sure beats have the monkeys from sysadmin bollocks around for a whole day on getting the config 'correct', only to find out when it's too late that they misunderstood something.
If you're going to pay for redundant power supplies, redundant cooling, RAID hard drives and dual NICs to make sure your hardware is done properly, then what's another $3k to make sure your intrusion detection works properly and you can call someone for help if it doesn't?
(Of course I'm assuming HP will actually answer the phone....)
One is tied up in this contractual mess, but the other, InnoDB has no such issues, and may even be faster for many purposes.
We did recently quite a bit of Perl development using MySQL and InnoDB tables, and they worked (surprisingly) well. Having transactions (finally!!) in MySQL is a huge blessing.
Somewhat related...while the article mentions that MySQL and Postgres don't have the large application development support infrastructures that the bigger commercial database have, they can be a lot quicker to prototype and develop with because of their relative simplicity.
We're in the middle of migrating our application to DB2 on RS/6000, and I have to say I'm missing MySQL's simplicity of administration and configuration...you can try out a lot of new ideas quickly with MySQL, whereas a big chunk of our time at the moment is spent poring over DB2 manuals for obscure command switches and SQL options (the LOAD utility can be a barrel of laughs for newcomers)...of course if our DBA was a little more competent, but that's a different story:-(
(And yes I do realise DB2 is much more powerful/robust...I'm talking about ease of development and rapid prototyping!)
In addition to the exciting news that NASA had broken a flying wing record, Slashdot editors publically announced a new Zero Wing record, with the 1 millionth "All Your Bases Are Belong To Us" post being officially recorded today.
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This sort of stuff makes me laugh. If only a computer was 1/10th as complicated as a cell. I find it is more the people trained in computer science who experience the shock when they come into a lab environment and see how complex, chaotic and large the biological data sets are that are routinely generated.
In my experience it is a rare computer scientist who can make the transition into bioinformatics and be truly effective, ie: not dependent on having a biologist sit with them 8 hours a day telling them what to do and why they're doing it, and can actually understand the breadth of the problem they're trying to solve, not just "develop a system to correctly pick these monoisotopic mass spectrometer peaks" or "build an algorithm to count the number of protein spots on a 2D gel"
It reminds me of a quote I saw published in a newspaper a while ago by an academic:
Biologists tend to write terrible computer code, but the computer scientists trivialise things and spend vast amounts of time solving problems that don't exist
I'd bid for it as long as it didn't include any annoying sidekicks that got in the way of your driving and always died at inopportune moments.
Interesting what the author was saying about 2.2 versus 2.4 in terms of stability. We have 3 Linux machines which are used quite heavily here at the moment:
1) A dual PIII-800/Intel 440GX/512MB ECC RAM based server, with a Mylex AcceleRAID 170 adapter, an Adaptec AIC-7896 SCSI adapter, Intel EtherExpress Pro 10/100, and an external 450GB SCSI RAID-5. This box is used for NFS/Samba file serving and an e-mail server for around 100 users.
It runs kernel 2.2.17
2) A dual PIII-800/VIA 133 server/1GB PC-133 RAM server, with an Initio A100U2W SCSI adapter, Intel EtherExpress 10/100 and 70GB of external SCSI RAID 1/0. It runs MySQL, Apache, and a collection of internally developed Perl, C and Java server apps, on kernel 2.4.3
3) A dual PIII-450/Intel 440BX/512MB PC-100 RAM server, with an Adaptec 2940UW adapter, Intel EtherExpress 10/100 and 170GB of external SCSI RAID-5. It is used as a development system, and runs MySQL, Apache, and assorted Perl, C and Java apps, on kernel 2.4.1.
Systems 2 and 3 have both been up for 197 days as I type this, and would have been up for over 250 days had we not needed to power them down to move them to a new server room.
System 1 (with the 2.2.17 kernel) has never stayed up for more than 55 days. It hard crashes without anything informative being written to the logs, and obviously required the reset button to be pressed.
Has anyone got any ideas, given the hardware configs and software running on these machines why 2.2 is so horrendous, yet 2.4 so stable?
Then Sun decided to release their Ultra 5 workstations at 6k a piece or so, IIRC. The market for Solaris x86 went **POOF** in about 4 seconds. The damn things are real live UltraSparcs and they work like a hot damn.
Ouch. If your Ultra 5 worked like a hot damn I'd hate to see how slow your x86 Solaris boxes were. We have some of the original 270MHz Ultra 5s around here at work and they're disgusting to use. I haven't used one of the new Blade 100s yet, but I hope their IDE performance and graphics are better than the Ultra 5.
Anyone here used both an Ultra 5 and a Blade 100 for any length of time care to comment?
why not just move distributions over to dpkg/apt/DEB management like Debian, or FreeBSD-style ports
Riiiiigghht. And that will happen straight after Debian adopts the graphical Mandrake installer, which is completely superior to Debian's tired old offering. It's all free software, after all, isn't it?
bloated -- it comes with the kitchen-sink *AND* the kitchen-sink-devel RPMS installed by default, for Pete's sake
and that's the reason you wouldn't recommend it? what sort of admin does a default install of anything? are you installing a mail server? a file server? database? DNS? you've always gotta do some customisation, and when you do, mandrake is no more bloated than any of the other distros.
155 million rows here on a dual-processor IBM p620 with 2GB RAM and DB2 v7.2 and it screams along. get the right indexes and buffer pool settings and there's no problem.
We've just done exactly the same thing. I miss MySQL's overall simplicity...it makes it really easy to develop quickly. after 6 momths of using DB2, i still feel like it's more in the way than actually helping me get the app developed.
there's no way we can go back now either...we're an IBM strategic partner (but the upside of that is we get nice hardware to play with for free...where's the Regatta?)
Last I checked, every "l33t" hacker and his 10 year old friends consider AIX to be a "crappy" version of Unix.
I'm guessing your 'l33t' friends don't like a really rock solid journalling filesystem, a damn useful logical volume manager included in the base OS, support for logical hardware partitioning, scalability into the stratosphere, bundled Linux toolkit, and probably the most comprehensive GUI admin tool ever built.Why the hell would you want to run Linux on a machine like the p690?!?!
i will admit though that having to pay extra for an ANSI C/C++ compiler sucks...
On the other hand, it meant that most people who used OS/2 had a handle on right-clicking.
having to drag things around on the desktop with the right mouse button took a lot of getting used to as well...or am i remembering the workplace shell incorrectly?
TV tuner - DV camera does the job *much* better.
except that a TV tuner card here in Australia costs under AUD$200, and a DV camera costs well over AUD$1500...in fact it may well end up costing more than the iMac.
The only other thing you'd want PCI for is for a second video card and that could be done through firewire if you really wanted
a video card running over FireWire? please...AGP was supposed to be a step up over PCI...going to less than 50% of the available bandwidth of PCI for a video card really isn't a step in the right direction.
Sure FireWire and USB can cover most bases...but even having one PCI slot would be an incredibly useful addition to the iMac, and wouldn't consume a lot of motherboard or case space.
So instead of a bluescreen or a kernel panic message, this thing will just flail its arms about yelling "Danger Will Robinson"?
Really, what else do you need PCI/ISA for?
Extra NICs? SCSI adapter? TV tuner?
Some posters here have mentioned that the fact that KOffice is free will be a significant factor in drawing people away from Microsoft Office. I'm not sure that's at all correct...A year or two ago, I remember seeing copies of Lotus SmartSuite 97/Milennium bundled with all sorts of PCs (not just IBM PCs), and OEM versions being advertised everywhere for AUD$30 (that's only about US $15).
SmartSuite 97 is probably still ahead of KOffice in terms of compatibility and features, plus it actually contained a famous component (Lotus 1-2-3), and it wasn't enough to stop it from sliding into complete obscurity.
KOffice (and StarOffice for that matter) have probably each got another 2 years or so of catching up before they even get close to where the now extict competitors of MS Office were a number of years ago...and being almost free didn't help them back then either.
that's exactly my experience too. can people here tell me...is it normal to waste days trying to compile stuff on AIX that compiles cleanly and without difficulty on Linux or Solaris? the Linux toolkit that comes bundled with AIX 5L is a little bit of help, but as the previous poster implied, stuff like gcc and bash doesn't really sit quite right with the rest of AIX, which can lead to some WeirdShit (tm) down the track when you're trying to compile supposedly 'standard' software.
Building Linux Clusters wasn't all that great either. I think they've withdrawn it from sale.
Ok...no network, no keyboard, no floppy, no CD-ROM, and locked up in a sealed room. Totally secure!
Windows 2000? It comes with a telnet server too.
You're not doing your friends any favours by recommending they get low-end machines. What happens when they decide they want to run their new copies of Windows XP and Office XP with all the bells and whistles and voice recognition turned on? Or use that Firewire port for something and start messing around with some funky video effects processing? Or play the latest flight-sim or FPS at full-res and maximum reality and physics? A fast CPU isn't everything, obviously, but it's sure as hell not going to hurt.
Software almost never gets faster, and consumer-type applications, like games and multimedia are some of the biggest CPU/graphics hogs outside of 'professional' level computung. I always recommend to friends to get the fastest machine they can afford. It might seem like overkill now, but you can bet in 12 to 24 months it won't be looking like an extravagance. Not everyone wants to run vi to edit C source code and marvel at how small and lean they can get their Linux kernel down to...
hmmm....the new Pocket PC OS is codenamed 'Merlin', and will contain speech recognition technology. that sounds exactly the same as OS/2 Warp v4.0. OS/2 lives! undoubtedly the Pocket PC OS 2003 edition will be based on CP/M, and feature floppy disk technology.
Linux combined with a TV...now there are even fewer excuses for the average lard-ass open source hacker to get outside and away from staring at a screen. Although...being able to watch an episode of Buffy while StarOffice starts up could be useful...
It's clear from the postings of a lot of people on this discussion to the effect of "your sysadmins must be all morons if they can't install snort and harden a linux distro themselves!!" that they've never had a sysadmin job in a big, busy company. It's simply not an efficient use of your time to be configuring and installing stuff like snort, or manually hardening a linux distro, when for $3000 you can have it all done for you, and backed by a company like HP.
Is it really worth to pay $3,000 for a distro with an Intrusion Detection System like snort [snort.org] configured ?
I'd say the distro would pay for itself in about 2 seconds if it actually did what it is advertised to do. $3000 isn't much to pay to have HP say "This thing is guaranteed to be configured correctly, and work as advertised.
Sure beats have the monkeys from sysadmin bollocks around for a whole day on getting the config 'correct', only to find out when it's too late that they misunderstood something.
If you're going to pay for redundant power supplies, redundant cooling, RAID hard drives and dual NICs to make sure your hardware is done properly, then what's another $3k to make sure your intrusion detection works properly and you can call someone for help if it doesn't?
(Of course I'm assuming HP will actually answer the phone....)
We did recently quite a bit of Perl development using MySQL and InnoDB tables, and they worked (surprisingly) well. Having transactions (finally!!) in MySQL is a huge blessing.
Somewhat related...while the article mentions that MySQL and Postgres don't have the large application development support infrastructures that the bigger commercial database have, they can be a lot quicker to prototype and develop with because of their relative simplicity.
We're in the middle of migrating our application to DB2 on RS/6000, and I have to say I'm missing MySQL's simplicity of administration and configuration...you can try out a lot of new ideas quickly with MySQL, whereas a big chunk of our time at the moment is spent poring over DB2 manuals for obscure command switches and SQL options (the LOAD utility can be a barrel of laughs for newcomers)...of course if our DBA was a little more competent, but that's a different story :-(
(And yes I do realise DB2 is much more powerful/robust...I'm talking about ease of development and rapid prototyping!)
In addition to the exciting news that NASA had broken a flying wing record, Slashdot editors publically announced a new Zero Wing record, with the 1 millionth "All Your Bases Are Belong To Us" post being officially recorded today.