[pygr-notify] [pygr commit] r239 - Edited wiki page through web user interface.
codesite-noreply at google.com
codesite-noreply at google.com
Tue May 26 13:09:19 PDT 2009
Author: cjlee112
Date: Tue May 26 13:08:31 2009
New Revision: 239
Modified:
wiki/DevelopmentRoadmap.wiki
Log:
Edited wiki page through web user interface.
Modified: wiki/DevelopmentRoadmap.wiki
==============================================================================
--- wiki/DevelopmentRoadmap.wiki (original)
+++ wiki/DevelopmentRoadmap.wiki Tue May 26 13:08:31 2009
@@ -1,7 +1,29 @@
#summary Outline of plans for Pygr's future development.
-= Background =
-First, to put this all in context, let's review the new features added in
the v0.7 release
+= Planned Release Milestones =
+
+== v0.9: NLMSA Joins ==
+In a
[http://groups.google.com/group/pygr-dev/browse_thread/thread/0d4d02149022e5a6?hl=en
number of discussions], we have already gone into some detail about new
possible features for NLMSA. The main idea is to define general purpose
JOIN operations that execute in a high-speed, scalable way, obviating the
need for researchers to write their own Python code (slow and possibly
buggy) every time they need to find some intersection between two or more
datasets. The result of an NLMSA join will of course just be another
NLMSA. The goal is to make alignment and annotation query a killer app in
terms of speed, query capabilities and ease of use.
+
+New features:
+ * ID standardization: adopting a convention for keeping IDs for sequence
sets consistent across different NLMSAs will greatly speed up JOIN
operations
+ * JOIN operations implemented in C
+ * more "Allen Logic" interval query operators for convenient query
+ * Python interfaces for join operations, possibly as a graph query
+
+== v1.0: Worldbase Extensions ==
+[http://www.doe-mbi.ucla.edu/~leec/newpygrdocs/tutorials/worldbase.html
worldbase] is a powerful concept for sharing data, but needs additional
tools and refinement. Currently, it is not easy to manage worldbase
resource databases, e.g. to copy resource or schema entries from one
[http://www.doe-mbi.ucla.edu/~leec/newpygrdocs/reference/metabase.html
metabase] to another, group them, delete them etc.
+
+New features:
+ * worldbase makerules: initially this could be implemented as simple
construction rules a la SCons for building some type of resource from some
types of dependencies.
+ * worldbase security via Signed Pickles: Python pickles create potential
security vulnerabilities. One simple and general solution is to create
digitally signed pickles using OpenPGP that can be verified with the
author's public key. This would then integrate with standard tools (e.g.
GnuPG) for listing sets of people whose content you trust.
+ * metabase management tools for viewing, copying, organizing, deleting
resource and schema entries between metabases. These should work
transparently with local resource metabases, SQL metabases, and remote
XMLRPC metabases (all using authentication).
+ * DNS-like framework for servers to share name lookup info with each
other
+
+= Past Milestones =
+
+== Pygr 0.7 ==
+new features added in the v0.7 release
* pygr.Data
* XMLRPC services (NLMSA, BlastDB)
* in-memory NLMSA
@@ -12,24 +34,22 @@
In short, an enormous number of different areas of new features were roped
together under the "0.7" label. This had a logical basis, namely that
pygr.Data drove a wide-ranging unification of many different things so that
they would all work seamlessly with pygr.Data.
-Going forward, I think it would be better for each "point release" to have
a better defined (and smaller) scope of new capabilities. This will make
our development process a bit more disciplined and understandable to
others, facilitate our testing, and make things go faster, I hope. In this
spirit, here are some ideas for the next point releases.
-
-= Planned Release Milestones =
-
== v0.8: Enhancement & Clean-up Release ==
+*The 0.8 feature set is done*. See the documentation for a list of its
[http://www.doe-mbi.ucla.edu/~leec/newpygrdocs/whatsnew.html new features].
+
V0.7 was very much a "developer release" in that it was a constant stream
of new features. I propose that v0.8 be more a "production release" that
is less about new features and more about ensuring that the most used
features -- alignment and annotation data -- work really smoothly and
easily for a typical Python programmer. I propose that this release would
concentrate on the annotation and testing projects that we already have.
The goal for this release is to define several areas where developers other
than myself can easily contribute to Pygr:
* add new sources of annotation data (e.g. Ensembl)
* add new sources of alignment data (e.g. programs like CLUSTAL etc.)
- * add new resources to pygr.Data
- * add web interfaces for searching / browsing contents of a pygr.Data
server
+ * add new resources to worldbase
+ * add web interfaces for searching / browsing contents of a worldbase
server
New features:
* pygr.Data auto-download capabilities (download=True mode) - _done_
* SQL support for other databases besides MySQL, e.g. sqlite - _done_
* support for read-write access to SQL databases - _done_
- * simple browsing / searching HTTP interface for pygr.Data server -
_deferred_
- * simple management functions over SSL XMLRPC - *not done*
+ * simple browsing / searching HTTP interface for worldbase server -
_deferred_
+ * simple management mechanism for XMLRPC services - _done_
* XMLRPC annotation services - _done_
* classes supporting Ensembl annotation (in support of Jenny & Rob's
project) - _done_
* additional UCSC alignment format(s), e.g. supporting hg18/hg17 mapping
- _done_
@@ -37,26 +57,7 @@
API Clean-up:
* define an "alignment parser API" that makes it simple to add a parser
for an arbitrary alignment format, and have the results automatically
loaded into an NLMSA. - _done_
* ensure that dict-like interfaces in Pygr properly support all the
standard Mapping Protocol methods - _done_
- * greatly expanded test suites courtesy of Rachel, Alex and Titus - *in
progress*
+ * greatly expanded test suites courtesy of Rachel, Alex and Titus -
_done_
* other clean-up and bug fixes - _done_
For details on current status, search the Issues database for label
[http://code.google.com/p/pygr/issues/list?can=1&q=label%3AMilestone-Release0.8
Milestone-Release0.8].
-
-== v0.9: NLMSA Joins ==
-In a
[http://groups.google.com/group/pygr-dev/browse_thread/thread/0d4d02149022e5a6?hl=en
number of discussions], we have already gone into some detail about new
possible features for NLMSA. The main idea is to define general purpose
JOIN operations that execute in a high-speed, scalable way, obviating the
need for researchers to write their own Python code (slow and possibly
buggy) every time they need to find some intersection between two or more
datasets. The result of an NLMSA join will of course just be another
NLMSA. The goal is to make alignment and annotation query a killer app in
terms of speed, query capabilities and ease of use.
-
-New features:
- * ID standardization: adopting a convention for keeping IDs for sequence
sets consistent across different NLMSAs will greatly speed up JOIN
operations
- * JOIN operations implemented in C
- * more "Allen Logic" interval query operators for convenient query
- * Python interfaces for join operations, possibly as a graph query
-
-== v1.0: pygr.Data Extensions ==
-pygr.Data is a powerful concept for sharing data, but needs additional
tools and
-refinement. Currently, it is not easy to manage pygr.Data resource
databases, e.g. to copy resource or schema entries from one database to
another, group them, delete them etc.
-
-New features:
- * pygr.Data makerules: initially this could be implemented as simple
construction rules a la SCons for building some type of resource from some
types of dependencies.
- * pygr.Data security via Signed Pickles: Python pickles create potential
security vulnerabilities. One simple and general solution is to create
digitally signed pickles using OpenPGP that can be verified with the
author's public key. This would then integrate with standard tools (e.g.
GnuPG) for listing sets of people whose content you trust.
- * Pygr.Data management tools for viewing, copying, organizing, deleting
resource and schema entries between pygr.Data resource databases. These
should work transparently with local resource databases, MySQL resource
databases, and remote XMLRPC resource databases (all using authentication).
- * DNS-like framework for servers to share name lookup info with each
other
\ No newline at end of file
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