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?
  

• My output keeps comming up blank
• When I choose an item in Help, bioLegato seems to freeze
• Why does bioLegato make me type in a file name, rather than giving me a file chooser?
  

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 bioLegato 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 bioLegato 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 or other packages etc... - You shouldn't have to choose. Just about any software package can be integrated into BIRCH. That being said, BIRCH is distinct from other bioinformatics packages in a number of ways:
• The bioLegato interace unifies the access to all programs in a single graphic interface. Behind the scenes, bioLegato takes care of
•  interconverting file formats, allowing transparent pipelining of data from one program to the next
• has workarounds for numerous bugs and features that can be problematic with many of the well-known programs that are in common use
• makes it easy to re-do analyses and ask "what if" questions
• automatically runs CPU-intensive programs such eg. phylogeny at a lower priority, preventing these jobs from interfering with the work of others on the system
• adds inormation to output that is not always available from the programs themselves. Examples would include parameters used during the run, and execution times for long-running jobs
• BIRCH organizes the documentation for many different bioinformatics packages into a well-organized set of HTML pages.
  
• BIRCH is highly flexible and configurable. It lets you add just about any program, documentation, or sample datafiles that you want, so that they appear seamlessly to the user as part of BIRCH and bioLegato.
  
• 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/socs/birch, you would type
  

  /home/socs/birch/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/socs/birch, you would type
  

  /home/socs/birch/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.
  

• 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.
• When I choose an item in Help, bioLegato seems to freeze? - bioLegato isn't frozen, it's waiting for you to click the tiny "Run" button that is somewhere on your screen, if you look for it. We will eliminate this button an the next release of bioLegato. In the mean time, sorry for the inconvenience.
  
• Why does bioLegato make me type in a file name, rather than giving me a file chooser? - This was necessary for backward compatibilty with existing GDE menus, which have no syntax to specify a file chooser in the menu. We have figured out a way to add a file chooser but retain GDE compatability. That feature will be in the next release of bioLegato.