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Software for using a computer for a course at CBS


There are several solutions depending on your situation and also a big overlap between solutions.
The solutions presented here are freeware - pick one that fits you.
Solutions are ranked after the ease of installation/use for a non-technical person.
Note: If you are somewhat serious about using linux, then virtualising Ubuntu linux with Virtualbox is really the way to go.

I have a Windows computer

I have a Mac computer

  • I need to login to CBS servers: 1) Mac
  • I need to login to Kbar and Gbar unix servers: 1) Mac
  • I need to login to Kbar and Gbar Windows servers: 1) ThinLinc
  • I need to login to Kbar and Gbar unix and windows servers: See above
  • I need to transfer files between my own computer and another server: 1) CyberDuck
  • I need to run unix/linux on my computer: 1) Mac
  • I need to run windows on my computer: 1) VirtualBox

I have a Linux computer

  • I need to login to CBS servers: 1) Linux
  • I need to login to Kbar and Gbar unix servers: 1) Linux
  • I need to login to Kbar and Gbar Windows servers: 1) ThinLinc
  • I need to login to Kbar and Gbar unix and windows servers: See above
  • I need to transfer files between my own computer and another server: 1) Linux
  • I need to run Windows on my computer: 1) VirtualBox

I do not have a computer

I need some other tools


Solutions

SSH+X: Secure shell and X-server

For accessing remote unix computers from windows you need a secure shell client and a X-server (for the graphical user interface) running. The X part requires a good connection, while the terminal (shell) part can be done on a modem.

MobaXterm
MobaXterm is great program that combines a simple terminal capable doing ssh and scp and and X-server. Download here. You can choose to download a installation package or a portable program (for those with no rights to install programs) which could even be run from a USB-stick. When you run the program, Windows Firewall will block some features of MobaXterm and ask if they should be allowed. Yo can easily let the firewall continue to block, as it does not matter for the part of the program that you will be using most. If really necessary you can unblock later.
When starting a ssh session to a remote server, you will be asked for the password again to use in a sftp session. You can cancel that if you don't want to transfer files back and forth between your computer and the remote server.
Here is a short downloadable instruction video for installing and using MobaXterm made by Daniel Edward Perez from Michigan State University.
You can also download "plugins" to MobaXterm, among those Perl, Python, Curl and Nedit.

Secure Shell Client - outdated
You can execute command on the remote machine with one part of the package and upload/download files with another part of the package. Nice GUI, but the software is no longer available from the creators: www.ssh.com. Download an old version here.
INSTALLATION:
Make a standard install and start the SSH client.
Add a new profile - name it CBS.
Edit the profile. On the 'Connection' tab use 'cell.cbs.dtu.dk' or 'organism.cbs.dtu.dk' as host name and your assigned user ID as user name (this will be sent to you before the course starts). Compression should be set to 'zlib' and terminal answerback to 'Xterm', press OK. If you experience "e;Algorithm negotiation fail"e; then set Compression to 'None'.
Edit the profile again. This time choose the 'Tunneling' tab. Mark the checkbox 'Tunnel X11 connections' and press OK. In case you want to get smart and do both 'Connection' and 'Tunneling' tabs at the same time - don't - it does not work. Tunneling should be checked in all profiles and the "quick connect". Tunneling gives the unix GUI.
Save your settings (the floppy).
Whenever you want to connect to the CBS server you just start the SSH client and choose the CBS profile and write your password. First time you connect you are asked to accept a server key - just do it.

PuTTY - replaced by MobaXterm
This does what Secure Shell does, just a bit different, and it can be integrated whih Xming. It is maintained software but not as intuitive as the one above. Download here.

Xming - replaced by MobaXterm
This X-server works great together with Secure Shell Client or PuTTY, as it provides the graphical user interface used in unix (X), when X is tunneled. Download here. You need Xming and Xming-fonts.
INSTALLATION: Do a standard install - yes to all, but DON'T start the server (last question).
When installing Xming Fonts, you will be told that there already is a Xming folder, and if you want to install on top of that. The correct answer is YES.
When you run the program use "Xming" in the start bar.
When you are running a small X will appear in your systray.

Errors
There are generally three errors. When starting an X-program, like clustalW or nedit, you get the message: "X connection to localhost:21.0 broken (explicit kill or server shutdown)." This means that your X server (Xming) is not running.
When starting an X-program, you get the message: "Error: Can't open display:" This means that SSH/Putty is not tunneling X correctly. You must check your settings again.
When starting an X-program, you get the message: "Unable to load critical font" or similar message complaining about fonts. This means that you did not install Xming Fonts correctly. Look at the guide again.
Some people worry about the question from windows firewall asking to either allow or deny access to the internet from Xming. The answer does not matter, so say whatever you like.

ThinLinc

ThinLinc is client/server solution. It requires that the server runs on the computer you want to connect to, which limits the solution to accessing Campus databar servers, both unix and windows. ThinLinc "transports" a picture of the "screen" on the remote computer to you, and as such it requires a good bandwidth for best performance. Download a ThinLinc client for Windows, Mac or Linux here. This is the Gbar download site. The official ThinLinc site, http://www.cendio.com/downloads/clients/, has newer versions of the client that does not work with the servers on the databar.

R

The statistical language/package R has both precompiled binaries for Windows, Mac and Linux and the source code available. Download here.. For more information on R, please consult http://www.r-project.org/

Perl

If you ask about Perl, then your native OS did not come with it. Most likely you are running windows. Download a windows version from http://www.activestate.com/. You can find a free version, and you can buy one with more bells and whistles.
Mac either has perl installed or it can be downloaded somewhere on Apple's homepage. You can find the source code to Perl at http://www.perl.org/ among other good info.

Java

Download Java here for all platforms. From this site you can also find more information on Java and Java Development Environment.

Python

You are not using linux, I see. Download Python here for Mac and Windows.

Cytoscape

Download Cytoscape here for all platforms. Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization.

Windows Services for UNIX

Surprisingly Microsoft has released a large package of software into the free domain, which actually turns your windows PC into a unix platform. You get among other tools a nice Perl. Download here.

Cygwin

This is a unix build for windows. Down load at http://www.cygwin.com/. The setup is fairly simple, but remember to pick the packages you need, like Perl. You could do a full install which is 600 Mb. Cygwin has a X-server included. It is not great, but serviceable. However, the Cygwin X-server has support for openGL. Some unix programs require that to work, and no other windows product (I know) gives that for free.

Borrowing a laptop

Some courses offer to lend you a laptop during course time. This laptop will be run Windows and it will generally be equipped with the tools you need, like SSH plus X-server and ThinLinc for accessing remote servers, Microsoft Office, Cytoscape, etc.

Using a stationary PC

Some courses will run in locations - typically building 210, room 052 and 152 - where stationary PC's are already present. You can log on with your campus id to these and run Windows. There are many different software packages (prepacked) that you can install on these machines, if they are not installed already.

Linux

Linux is Unix. Using linux as OS will free you from a whole set of (connectivity) problems you might have with Windows, but most likely create a new set of problems. You can install linux either natively on your computer or as a virtual machine, see VirtualBox.
There are many different linux distributions, some free, some not. Download a CD/DVD image from OpenSuSE, Fedora, Debian or Ubuntu.
Ubuntu has proved itself to be the easiest installation - a first time linux user would do well to choose that. If you install natively, then you need to burn the image first to a CD/DVD. If you plan to run virtualized linux with VirtualBox then choose a 32 bit image (ISO file) and download that.
Linux will give you Perl, Python and SSH automatically among a very large set of tools. Do you want to run your web server - here is your chance.
Login to other computer; ssh -X username@remote.machine.name
File transfer: sftp username@remote.machine.name

Windows

If you need to use Windows on your not-Windows machine, then you need a Windows Installation CD, no matter if you want to run Windows natively or virtual, see VirtualBox. Apart from that it is installation, "as usual".

Mac

So you have a Mac - good for you. Mac is running natively unix behind all that eye candy and over-userfriendly interface. You just need to learn to use it. Getting access to the unix part of the Mac is through the "Terminal" application. To access remote computers through the command line on the terminal use: ssh -Y username@remote.machine.name, i.e. ssh -Y stud003@login.cbs.dtu.dk
If you are using OSX version 10.5 ("Leopard") the X11 application is installed by default. If you are using OSX 10.4 ("Tiger") or 10.3 ("Panther") X11 is either on your install disk or you will have to download it from Apple and install it. Check this page for instructions.

VirtualBox

VirtualBox from Oracle is a wonderful tool. It installs a package that will allow you to run one or more virtual machines on your computer. On these virtual machines you can install any OS you want, see Linux or Windows. Examples: You have a Mac, you want to run Windows - use VirtualBox and you can run Windows in a Mac application window. You run Windows, but would like to run linux for some specific purpose - same answer.
If you don't need your virtual machine (VM) anymore - throw it away and release the disk space for some other purpose. A virtual machine does not need much disk space (5-10 GB), since it can access the disk on the native machine. You can simply share files between your host machine and virtual machine. You can even copy/paste between them, once you have installed the VBoxGuest additions. There is approximately a 10% performance loss when running virtual, but it is worth it for the ease of use. There are other free virtualizing softwares, like VMware Player (one of the first softwares on that market and still very strong), but VirtualBox has proved itself to be small package that is very easy to use and install. No support from CBS will be available on anything but VirtualBox.
Download VirtualBox for Windows, Mac and Linux versions.
Installation: Do a standard install. There will be several warnings from Windows about using drivers that has not gone through a Microsoft approval step - these can safely (and must) be ignored - just click Continue. When creating a new virtual machine, you must first decide what to install as a guest OS. The recommended choice is 32 bit Ubuntu linux. In any case you should probably go for 32 bit OSes. Secondly, you must decide how large a disk you should use - the default 8 GB is fine. You must also decide how much memory you should allocate to the VM; if you only have 2 GB RAM on your "real" machine, then allocate 768 MB, if you have more real RAM then allocate 1024-1536 MB. Before you launch your new WM, you must insert the installation image for the OS (Ubuntu) you downloaded into the VM's CD-rom drive. This is done under 'Storage' for the VM - it can be a bit tricky to find the small icon for the CD-drive, but when the standard "choose file" menu opens, then you hit it right.
After installation of your virtual OS, you must also install the 'Guest additions'. These can be found under 'Devices' when your guest OS is running. It will give you much better screen control (resizing), faster screen updates, the ability to cut/paste text and share folders between your host OS and guest OS.

LiveCD

A liveCD is a CD/DVD that contains a complete bootable linux environment. The environment is able to access your harddisk, so whatever you do can be saved. This is a superior way of learning linux at the cost of one CD. You get everything without installing anything at all. There are several versions with different capabilities, but which one is best is hard to say.
Download Knoppix
Download SuSE liveCD
Download Quantian scroll down.

WinSCP

WinSCP is a wonderful tool if you just need to transfer files back and forth between computers. It may be a little hard/diffucult to configure so it is really easy to use, but fortunately you don't have to do so. It will still work well, but you might miss out on the fancy stuff. If you need to update a file on the remote machine, then transfer (copy) the file to your desktop, make your changes, transfer the file back and finally delete your local copy. Even if it looks like you can just doubleclick on the file, and it might even succeed, then it is bad practice.
WinSCP can be downloaded at http://winscp.net.

CyberDuck

CyberDuck is a general file transfer/remote file access tool for Mac. It does what WinSCP (above) does and more. THE tool for Mac.
CyberDuck can be downloaded at http://cyberduck.ch/.


GETTING HELP

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