About BIRCH

• What exactly is BIRCH?
• Why should I choose BIRCH, as opposed to EMBOSS, GCG etc...
• Can I install BIRCH on my PC?
• Why don't BIRCH programs run through the BIRCH web site?
• Why is BIRCH available for Unix and not for Windows?
• Is there a way to install my own programs?
  

Setting up your account to use BIRCH

• How do I set up my account to use BIRCH?
• How do I turn off my BIRCH access?
• Does it matter which shell I use?
  

• Why can't I open the menus in GDE?
  
• My output keeps comming up blank
  

About BIRCH

• What exactly is BIRCH? - Actually, the best answer to that question is that BIRCH is a conceptual framework for building a bioinformatics system that is user-oriented, powerful, easy to use, and tailored to the needs of the local user community. That being said, what you get when you download BIRCH includes:
• A hierarchical directory structure that organizes programs, data and documentation
• A large set of pre-configured, ready-to-use Open Source programs for analysis of sequences, markers, genetic data, gene array data...
• The GDE graphic interface, which greatly simplifies working with large datasets, and is particularly good at using output from one program as input for another program. Think of GDE as a program that knows how to run other programs.
  
• A database of all documentation on the system that is readable through the BIRCH web site
• Tutorials that are task-oriented, showing how to put together several programs to accomplish a task, rather than focusing on the details of how to use each specific program. Tutorials include numerous screen shots with real data.  Tutorials cover the critical theoretical points, possible problems, as well as practial details of how to accomplish a complex task.
  
• A set of system administration tools that simplify the process of making everything work the same way for everyone
  
• Why should I choose BIRCH, as opposed to EMBOSS, GCG etc... - You shouldn't have to choose. Just about any software package can be integrated into BIRCH.
  
• Can I install BIRCH on my PC? - Well... yes, if your PC runs Linux. Otherwise, you have to use BIRCH on a Unix or Linux server. The great thing about BIRCH, though is that you can access your Unix account (and therefore, BIRCH) from any computer on the Internet. See Using Unix from Anywhere.
• Why don't BIRCH programs run through the BIRCH web site?
  
• Been there, done that - There are already more web sites than you can count that let you paste data into a window and run a program. BIRCH goes way beyond that.
  
• Web pages are ackward interfaces - For anything but very simple tasks, Web pages are not a very efficient way to work with data.
  
• the web program runs in your browser. It is not well-integrated with the rest of your desktop
  
• output is almost always human reable, and not readable by other programs
• you usually have to go to many different web sites to do a variety of tasks
• web pages are usually geared to working with one data item (eg. sequence) at a time, rather than large datasets.
• most web sites have to impose limits on the amount of processing you can do
• web sites are less secure, because your data goes off-site
  
• Why is BIRCH available for Unix and not for Windows? - The short answer is that the Windows platform is really specialized for a single user on a standalone PC. The Windows system is almost impossible to administer as a secure multiuser system, and multitasking is still quite unreliable on Windows XP. As well, the Windows interface is wedded to the "one program owns the screen" method of working. Unix has always been a multiuser, multitasking system, and Unix desktops have always been designed to give the user the ability to work simultaneously in many windows. (Mac users take note: Since OSX is a full Unix system, plans are in the works for a future BIRCH release for OSX.)
• Is there a way to install my own programs? - On any Unix or Linux system, each user can have a directory called 'bin' in their $HOME directory, in which they can install their own programs. You just need to make sure that $HOME/bin is in your $PATH. On some systems this is automatic. Just type 'echo $PATH' to see if a directory called 'bin' in your home directory is included. If not, you can add a statement like
  
  PATH=$PATH:$HOME/bin
  
  to your .profile file (if you use a BOURNE-type shell like bash) or
  
  setenv path $PATH:$HOME/bin
  
  to your .cshrc file (if you use a csh-type shell like tcsh). Once your bin directory is in your $PATH, any program you put into your bin directory will be found at the command line.
  
  

Setting up your account to use BIRCH

• How do I set up my account to use BIRCH? - You need to run the newuser script which is found in the directory $BIRCH/admin. For example, if BIRCH was installed in /home/psgendb, you would type
  

  /home/psgendb/admin/newuser

• How do I turn off my BIRCH access? - Run the nobirch script which is found in the directory $BIRCH/admin. For example, if BIRCH was installed in /home/psgendb, you would type
  

  /home/psgendb/admin/nobirch

• Does it matter which shell I use? - A lot of work has gone into making BIRCH shell-neutral, so you should be able to use any available shell. BIRCH has been tested using csh, tcsh, ksh, bash and sh. There is an issue with sh and ksh. It is impossible to get sh to display the current working directory ($PWD) in the command prompt, and to get that prompt to update each time you change to a new directory. ksh seems to be able to do this on Solaris, but I have not been able to get it to work using ksh on Linux. Therefore, on all systems, I would recommend against using sh, and on Linux, avoid ksh.
  

• Why can't I open the menus in GDE? - In GDE, the mouse buttons work as follows:
  
• use the left mouse button to select data, change menu items etc.
  
• use the right mouse button to open a menu.
• My output keeps comming up blank - There can be many causes for this, but the most common is that you forgot to select one or more sequences before opening a menu to launch a program.