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Version-2003.0-beta Release Notes

James Bonfield, Kathryn Beal, Yaping Cheng, Mark Jordan and Rodger Staden

This is the final official release from Rodger Staden's group at MRC-LMB, as despite receiving excellent referees reports and the highest possible banding, the last grant application was not funded by MRC. Rodger Staden is the only member of the group still at MRC-LMB. However we hope it is not the last ever release of the Staden Package.

One possibility is to release the package under an Open Source licence and MRC-LMB have agreed to allow this to happen. However this will only work if there are sufficient people to coordinate, maintain and develop the package. We urge anyone who is willing to participate in this project to communicate via the bionet.software.staden newsgroup (also accessable via Google and Bio.net). The staden-admin and staden-package email services will no longer be manned, so you must use the newsgroup.

An Open Source release would impede any chance of charging a small fee to act as an alternate way to cover further development. So although we would prefer the package to be Open Source we need to see sufficient and honest commitment before choosing this route. Further statements on this topic should be found (later, if not now) either on the Staden Package website and/or in the newsgroup.

All licencing code has been removed from this release so you do not need to use the licence form to request a licence file. We have also issued a licence for the 2002.0 release to unlock it for all hosts, so you are not required to upgrade to the beta release solely to obtain a licence free version.

Note that this is a "BETA" release. That means that it is work in progress which has been tested internally and has known bugs documented, but is not of the quality we would normally accept. Spin2 is very much "work in progress" and isn't even a BETA release. Hence keep the original spin. If this release works sufficiently well for you then that is good, but we would recommend you to keep the official 2002.0 release available too. Having both installed at once is possible, if a little tricky. See the appendix for details on this.

The primary new features in this release are:

Program version numbers

Operating systems

The binaries for this beta release have been created in the following build environments. Typically newer environments for the same operating system should work fine, but not necessarily older systems. (For example, the binaries will not run under RedHat Linux 5.x, but will run on RedHat Linux 7.x)

Demo data sets

These files were originally intended for demonstration of the package when running without a licence. This is no longer applicable, but they clearly still have a use for training purposes. Please see the course documentation in the course/*_docs/*.pdf files. All pathnames listed below are relative to the installation root for the package.

Here is a list of sequences which may be loaded into spin:

For a good example of protein-protein similarity plots, try using mysa_drome.seq and mysa_human.seq.

For dna-protein plots, try using cemyo1.seq against mysa_caeel.seq.

To see how spin handles large sequences try using ecoli.00003 and lambda.seq. This is a large comparison: 250Kb against 48.5Kb. Hence the slower searches, such as Find Similar Spans, will take a long time. We suggest searching with Find Matching Words using a word length of 12.

Gap4 data:

Appendix - multiple releases coexisting on the same machine

It should be possible to install multiple versions of the Staden Package on the same system.


For unix, this is just a matter of extracting the tar files in multiple places. You can only have one PATH environment variable, so you'll need to decide which version you wish to need to have as default.

There is a difference between the main tcl/tk programs (gap4, spin, etc) and small standalone utilities like vector_clip, screen_seq, etc. The small utilities sometimes require STADENROOT, STADLIB, etc, environment variables to be set, but generally not. The main tcl/tk programs are invoked via a shell script which automatically sets the environment variables if needed. Take for example gap4. It is a script that works out STADENROOT relative to where the gap4 script itself is, or by copying it from the STADENROOT_2003 (or STADENROOT_2002 for the 2002.0 release) environment variable. From this is defines all the other necessary environment variables. Finally it runs "stash $STADLIB/gap/gap.tcl", which is the heart of Gap4 itself.

Hence if you intend to write your own gap4 scripts (for example), invoking stash at the command line, you will need to manually ensure that the appropriate environment variables are defined. Otherwise they can safely be ignored.

Practically speaking, the bottom line is that for most users you can get away with doing nothing other than setting up your path. And so if your path contains /usr/local/staden_2003 (for example) as the default package version, then typing /usr/local/staden_2002/linux-bin/spin (for example) would start up the old version.


Windows uses an entirely different mechanism for starting the applications. The shortcuts use a program Staden Package utility called "run.exe". This sets up the environment variables and so is the windows analogy to the unix shell scripts. After setting up the environment run.exe does the same as unix - "wish.exe $STADLIB/gap/gap.tcl" for example. It uses wish instead of stash, but is the same otherwise.

So having two installations should also work under Windows. However there are a few tricky issues; how do we have two copies of the shortcuts and/or menu items? Each release will overwrite the previous release menu items. Therefore to install a second release without first removing the existing release you should first rename the Staden Package menu in the Start menu to something different (by adding a version number). This will allow two sets of menu shortcuts to co-exist.

The Windows registry can cause problems too as the package sets up a few keys to do with uninstalling and for file type association (so that trev starts up when we double click a ztr file, for example). The last release you install will have the file type associations, so plan the order accordingly.

The registry will also make uninstall tricky. If you decide to just install this beta release, but wish to keep the 2002.0 release, then it's probably best to uninstall both, tidy up any directories left, and then reinstall the 2002.0 release.

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