Version 5.0.2 Release Today

[Bill Longabaugh]

Version 5.0.2 has been posted. It addresses the bugs that have been
uncovered in recent weeks with the ImageGeneratorApplication command-
line mode and the Viewer start-up crashes, as well as a couple of
other issues.

The one new feature is that expression table entries can now be
optionally tagged as "Maternal", "Zygotic", or both. Nodes can then
be assigned to extract their expression data from just one of these
sources. For example, this permits a gene to be driven in a dynamic
submodel by just the "Zygotic" table entries, allowing it to ignore
expression table entries that are tagged as having "Maternal" origin.

Let me know if you have any questions or problems with the release!

-- Bill

[zuo]

Hi, I am trying to integrate some extra data into BTP file (experiment data & URL links). From website only CSV file format is described in detailed, where can I find some description about BTP format? many thanks.  Kind Regards   jié zuo   Email: po_...@yahoo.com Tel: +44 (0)1865 222470 Fax: +44 (0)1865 222501

[William Longabaugh]

Unfortunately, a BTP format specification document does not
exist, since the format really needs to be officially considered
to be in a permanent state of flux, with things always being
tweaked from one version to the next. The only "guarantee" is
that all future versions of BioTapestry should be able to read
all past BTP files. Sorry!

With that being said, I realize that sometimes the easiest way to
do some things is to edit the file directly, and I can always
provide specific info about any particular aspect in question.

My recommendation is typically to use a feature in the program,
then study the before-and-after BTP files to see how things
are handled. Since the file is XML, it is usually pretty
easy to see what is going on, especially using a graphical
diff tool like xxdiff.

In this particular instance, it seems the things you want
to add are typically entered using the right-click menu's
"Properties" option, then selecting the "Text Annotations"
or "Data URLs" tabs. As this BTP fragment shows, free
text goes into the <nodeFreeText> element, and any
URLs go into the <nodeURL> element for a gene. This
info is most simply added to just the first "Full Genome"
model in the file:

<nodes>
<genes>
<gene name="Gene 1" id="0" >
<nodeFreeText>Hello &lt;b&gt;world!&lt;/b&gt;</nodeFreeText>
<nodeURLs>
<nodeURL>http://www.biotapestry.org/index.html</nodeURL>
</nodeURLs>
<simulationLogic type="AND" />
</gene>
</genes>
</nodes>

Note that the free text feature supports basic HTML tags,
which are converted into HTML entities in the string (as in
the bold tags above).

As opposed to embedding large amounts of text in the BTP
file for each gene, people have found that using the
"Data URLs" option is the better way to go. That way,
the data is downloaded only when the user wants to see it.
When such a list is provided for the gene, BioTapestry
will access those URLs in order and display the concatenated
contents in the right-click Experimental Data page.
That way, you can maintain simple web pages on a web server
instead of having to directly edit the BTP file. A small
section of the V3 release notes gives some details:

http://www.biotapestry.org/docs/V3ReleaseNotes.html

One other thing to note is that the Experimental
Data page can only handle very simple HTML, and is
NOT a full web browser. If you provide actual
clickable links in the text, the user will not
really be able to navigate around (e.g. NO back
button is provided right now), and I cannot
guarantee that pages using e.g. CSS will display
well. It is mostly intended to support simple
web pages created by the user.

Hope this info helped.

-- Bill

zuo wrote:
> Hi,
>
> I am trying to integrate some extra data into BTP file (experiment data
> & URL links). From website only CSV file format is described in
> detailed, where can I find some description about BTP format? many thanks.
>
> Kind Regards
>
>

> ji� zuo
>