[Scriptome-users] New/updated Scriptome tools and protocols, a new volunteer, and m ore

Amir Karger akarger at CGR.Harvard.edu
Fri Feb 17 10:01:30 EST 2006

Hi Scriptome listeners,

It's been a long time since the last update, but we've been making progress.
I'm happy to announce an updated version of the Scriptome is available at
http://www.cgr.harvard.edu/cbg/prescriptome and should be moving to the true
Scriptome site within a few days. Here are the main changes, which are
expanded below:

* Four new calc tools, plus two more updated to work on Windows
* New FASTA protocols
* Introducing Jason Konrad, Scriptome Volunteer
* Excel Scriptome
* Backend work towards automated testing

There's also a bunch of minor changes to documentation, usability upgrades,
and typo fixes. (Also, thanks to Tom Snir for noticing that calc_row_sum
wouldn't run at all!)

There's a whole lot more to do on the Scriptome.  We've made big progress on
things like:
* "Explain This" buttons for each tool to help Perl novices (Jason),
* Boxes on the website for inputting parameters, so you don't have to edit
the tools on the command line, and
* The Excel project so you can skip the command line entirely (Eitan et al.)

Stay tuned for more announcements, and remember to email me or the
scriptome-users list with ideas, criticisms, bug reports, protocol
questions, or invitations to be an author on your latest paper that use the

ps Users within harvard.edu: You now need to type www.cgr.harvard.edu, not
just cgr.harvard.edu to get to the Scriptome website


New Calc Tools:
- Calculate length of a given column on each line (calc_col_length)
- Calculate length of a given column on each line (calc_col_length)
- Calculate how many times each value appears in a given column
- Calculate sum of values in a column for each value in another column

calc_num_lines and calc_num_fasta_records now work on Windows instead of
just UNIX/Mac.

New FASTA Protocols:

Several new protocols have been added to the Sequences page. A number of
users asked how to use Scriptome tools to filter and reformat FASTA tools in
certain ways. It turns out that using change_fasta_to_tab gives you a lot of
flexibility: you can then use the other Scriptome tools to manipulate
tabular data, and finally change_tab_to_fasta when you're done (if you

New Volunteer

Jason Konrad read the perl.com article about the Scriptome and volunteered
to help. He has done some good work to make the tools a bit simpler, which
will hopefully hit the website soon. He's also embarked on the larger
project of annotating the tools. This is the main obstacle to an "Explain
this" button, which is one of our most popular requests. Thanks, Jason! (If
anyone's wondering, there's plenty of other jobs we could find for more

Excel Scriptome

Eitan Rubin, co-creator of the Scriptome, has moved to Ben Gurion
University, but he and his colleagues continue to work on an exciting
project to embed Scriptome commands in an Excel spreadsheet, so you don't
need to use the command line at all.

Backend work

We've done some backend work to improve the Scriptome overall, and speed up
future development. The Scriptome is now hosted in CVS at
bioinformatics.org, so we can coordinate development. We've done some work
towards automated testing of the tools. We're gradually improving tool
documentation, as well as output messages.  

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