Specialized Knoppixes for Fun and Profit

An anonymous reader writes "The University of Puerto Rico High Performance Computing facility (HPCf) and the Puerto Rico Biomedical Research Infrastructure Network (BRIN-PR) are pleased to announce the release of bioknoppix. bioknoppix is a live CD linux, based on KNOPPIX, and specialized to include tools for bioinformatics. bioknoppix does not need to be installed on your computer, making it a perfect tool for workshops and demos. Some of the software included in the 0.3 release: EMBOSS 2.8.0, jemboss, artemis, clustal, Cn3D, ImageJ, BioPython, Rasmol, Bioperl, Bioconductor. For more information please see the bioknoppix home page." Reader Tussinator wrote in about a new release of ClusterKnoppix.

KnoppMyth is cool

[maharg]

http://mysettopbox.tv/knoppmyth.html [mysettopbox.tv]

Knoppix remastering made easy.

[khasim]

http://www.knoppix.net/docs/index.php/KnoppixRemas teringHowto

Build it the way you want and burn it!

Don't forget to grab an inexpensive USB memory toy and you have it all!

Re:Slashdotted.

[hortiz]

A bit torrent [upr.edu] of the iso and md5sum.

Mod parent up.

[khasim]

With Knoppix, as long as you can boot the CD, you have all the applications you need, pre-installed, pre-configured, pre-tested, pre-EVERYTHING.

It's all about the apps.

(and a rock solid OS to run the apps on)

Re:Lovely ideea, but...

[ibm5_25]

Check out Damn Small Linux [DSL] at

• http://www.damnsmalllinux.org
• • It's under 50 mb and perfect for carrying with you.

Re:how about knoppix recovery/security cdroms?

[smart.id]

Try Knoppix-STD [knoppix-std.org]. I haven't really tried everything on it, but it's supposed to be very good for doing security vurinabilities.

dyne liveCD

[Anonymous Coward]

There's another VERY good one out there for the media hacktivists but really not only, Dynebolic [dynebolic.org].
Give it a try it just gets where others dont (check for yourself the features) and for the lovers of the "beowulf of these" liners...

yes it does! Openmosix clustering in a boot.

Re:Lovely ideea, but...

[rindeee]

I think what you want is Flonix. It is EXACTLY what you describe.

http://www.flonix.com/

Getting to be a crowded market:

[dan dan the dna man]

Bio-Linux [bio-linux.net]
BioBrew [bioinformatics.org]
DNALinux [dnalinux.com]

I'm a developer for one of the above projects. Competition is interesting.

It's Knoppixe

[Anonymous Coward]

Sorry to put you down. But my vote, as native german speaker, goes to "Knoppixe".
The "e" is pronounced as a schwa vovel [wikipedia.org]. Plus the "K" is not silent!

my favorite knoppix distro/varient

[enrico_suave]

KnoppMyth [mysettopbox.tv]

Practically a linux PVR on a bootable CD...

E.

3.3 and my digital camera, wireless cards, etc

[jarich]

I've played with linux for years but never got the expertise level to make the fluff stuff work (scanners, cameras, etc). I can compile my own kernels, etc... but never the consumer devices. On my laptop, out of the box, my wireless card works. My wife's digital camera works. It has a utlity I used to resize my NTFS partition. It has a ~working~ DVD player and cd burner. I repeat, I didn't have to patch the kernel. I didn't have to download anything! This was easier that the last windows box I setup! I have ~never~ gotten this level of consumer usable Linux from anyone else.. not RH, not Mandrake, no-one. Go Knoppix! I've already given copies to 3 other Wintel users. :) This one is ready for prime time. btw, using the toram flag at boot time runs the whole thing out of memory! It's really fast! :)

An alternative...

[stm2]

There is an alternative distribution for bioinformatics. It is based on Slax [linux-live.org] (A live distro based on Slackware) and it's is called: DNALinux [dnalinux.com].
Disclaimer: I am one of the authors of DNALinux. The program is free as in GPL.

Re:Lovely ideea, but...

[hazem]

but why not go the whole nine yards? Put everything you need on a USB drive and boot from there!

If you're talking about those little USB-flash memory things like the Sandisk Mini-Cruzer [sandisk.com], that might only work for a while. I've read that these things can wear out [wikipedia.org] after so many writes. You'd be okay for booting, I imagine, but you'd want to avoid having any swap-space set up on the device.

Re:Knoppix remastering made easy.

[frovingslosh]

Don't forget to grab an inexpensive USB memory toy and you have it all!

And don't forget to make it look for that inexpensive USB memory by default, so you don't have to type in the "cheat code" every time you book, like you do on the regular Knoppix release.

Bioinformatics progs on CD but Rasmol?!

[Bowling Moses]

Okay, it's a pretty cool idea and it goes one step further than what my friends and I (grad students in biology or chemistry) have done on our own by putting useful biochemistry tools on a CD for when we travel. But Rasmol?! It's antiquidated and was replaced by Protein Explorer, a Rasmol derivative, three or four years ago. If you want a free, compact, powerful, and reasonably easy-to-use program that can be run on linux/mac/windows for viewing macromolecular structures then you use Deep View [expasy.org]
Swiss-PdbViewer. It can do a lot of what the molecular visualization programs we actually use to build protein structures (eg O, Xtalview) can do, plus you can use it to generate good-quality images by using POV-Ray.

Re:Lovely ideea, but...

[jhoger]

All media wears out eventually Flash media is typically good for 100,000 writes per sector.

You defintely wouldn't want to use it for swap space (Knoppix et al either don't use swap space or they can use the hard disk if there is one).

However, for small files like configuration of your email client, holding your keys, some documents, flash drives are good for that since that's what they are designed for.

Another specialization

[pummer]

In the Overclocking community, we use Overclockix [octeams.com], a distro specified for testing new overclocks and also using distributed computing apps without a hard drive.

Here's how to do something similar for Windows!

[WhoDaresWins]

If any of you were wondering how to do something similar with Windows then now you can! I realise that this being slashdot there are going to be flames about why would you do this etc? For the simple reason that not all porgrams are available on Linux.

Anyway coming back to the topic of how to do this for Windows. Well first of all there is this thing called Windows PE (Pre-installtion Environment) which is basically a Microsoft created bootable Windows CD for computer OEMs. Its basically a very stripped down version of Windows XP (or Win2K3) with just a command prompt and the ability to run some simple GUI programs. But this WinPE is normally only available to OEMs and system builders (but it isn't hard to find online retailers for it). However WinPE isn't very useful from a full usable system point of view. So someone has come up with a way to make your own customized WinPE like bootable Windows CD. All you need is the instructions and your own Windows CD to do it. Here's where you can find more information -

Bart's Preinstalled Environment (BartPE) bootable live windows CD/DVD [nu2.nu]

KnoppiXMAME

[antdude]

KnoppiXMAME [freshmeat.net] for MAME stuff. :)

Re:how about knoppix recovery/security cdroms?

[Vladimir]

Recently I realized just how easy it is to extend Knoppix if you're using DVD. First of all, you can burn Knoppix ISO on DVD and get a bootable system. It makes sense because DVD are generally faster than CD and system will use only 1/7 of the space so seek times are much lower. (Just for completness: to burn ISO on DVD+R/W, you just say "growisofs -Z /dev/dvd=/cdimage/knoppix.iso", et voila, it's done; may also work with "-R/W", but I'm not sure). Another nice feature of growisofs is that it can write the next session:
"growisofs -M /dev/dvd -r /usr/local/games" and all your games can be found in the root catalog (i'm sure mkisofs has an option to put it elsewhere)
So, you start with standard knoppix and add about 3.8GB of your favorite software: no need to repackage and create compressed isofs.

BTW, it also probably means that a malicious application can in theory alter Knoppix if it's on CDR/W, esp. if mkisofs and growisofs are included.

Re:Specialization

[mAineAc]

Here are a few Knoppix varieties for people to check out.

EduKnoppix [unicatt.it]
Gnoppix [gnoppix.org]
NordisKnoppix [broadpark.no]
KnoppMyth [hust.la]
Augustux [zaralinux.org]
Condorux [ourproject.org]
BitDefender [bitdefender.com]
FeatherLinux [berlios.de]
Flonix [osdisc.com]
Overckockix [octeams.com]
Knoppix STD [knoppix-std.org]
Sulix [homelinux.net]