ggonnella (Giorgio Gonnella)

You’re not logged in!
Login
Pricing & Signup

Name: Giorgio Gonnella

Email

Website/Blog: http://looks-interesting.blogspot.com

Location: Hamburg, Germany

Member Since: Aug 22, 2008 (about 1 year)

6 public repos
1 follower

Following 1 githubber and watching 10 repositories view all →

Public Repositories (6)

- 1
- 5
genometools

GenomeTools genome analysis system.

Forked from gordon/genometools Sat Aug 08 07:37:16 -0700 2009

Last updated Fri Nov 13 00:41:39 -0800 2009
- 1
- 1
ruby_progress_bar

a simple progress bar to give some feedback in console based ruby scripts

Last updated Wed Jun 03 05:22:38 -0700 2009
- 1
- 6
active_scaffold_list_filters

Filters for the Rails Active Scaffold Plugin

Forked from tvongaza/active_scaffold_list_filters Mon May 18 05:59:12 -0700 2009

Last updated Mon May 18 07:07:21 -0700 2009
- 1
- 1
genomeviewer

GenomeViewer is a webbased viewer for GFF3 genome annotations

Forked from gordon/genomeviewer Mon Oct 13 12:16:53 -0700 2008

Last updated Thu Mar 12 09:38:16 -0700 2009
- 2
- 0
boxover_helper

A rails helper to make easier to use boxover javascript library (http://boxover.swazz.org)

Last updated Sun Sep 07 01:39:02 -0700 2008
- 3
- 0
attr_hidden

Rails / ActiveRecord - Hide attributes in a model (particularly useful for Single Table Inheritance)

Last updated Sat Sep 06 08:06:39 -0700 2008

Public Activity

ggonnella pushed to assembly at ggonnella/genometools Fri Nov 13 00:42:01 -0800 2009

HEAD is e580c26368bd5a49e4c1ea1859504a8303da7cd4

139 commits »

ggonnella committed ebfc3353:

overlap enum values standardized (GT_OVERLAP_ prefix and upcase)
ggonnella committed fc18f951:

GtStringGraphVertexMark enum values standardized
ggonnella committed 290ca640:

typedef of string_graph types collected in an own header
ggonnella committed 3432df88:

implementation of string graph & tool to create a string graph from overlaps
ggonnella committed 37199477:

tool for the determination of all overlaps of all fragments in the input file
ggonnella committed 83cc832b:

simreads: improve -help messages
ggonnella committed b1ad5ea3:

simreads: added option to show progressbar
ggonnella committed b72bfb5c:

simreads: better error handling in gt_simreads_runner()
ggonnella committed ce0ffdc8:

simreads: added file options
ggonnella committed f8dd8c7c:

simreads: added email for bug reports
ggonnella committed 43545d13:

correct copyright year statement
Giorgio Gonnella committed 0cbd30ef:

simreads: removed some unused code lines
Giorgio Gonnella committed 280de44c:

simreads: -coverage option alternative to -num
Giorgio Gonnella committed b33b3b37:

simreads: added -erate option to specify a read error rate
Giorgio Gonnella committed dd94c633:

simreads: allow -maxlen to be equal to -minlen
Giorgio Gonnella committed 62f82e91:

simreads tool: simulate sequencing reads from known sequences
Sascha Steinbiss committed 82910006:

change image and wording on front page
Sascha Steinbiss committed f0d01f1b:

mention new Windows versions on website
Sascha Steinbiss committed 64cfe70f:

ltrdigest: add support for Pfam trusted and gathering cutoffs
Sascha Steinbiss committed e8310d9f:

do not fail on non-fatal condition

And 119 more commits...

ggonnella pushed to master at ggonnella/genometools Fri Nov 13 00:41:40 -0800 2009

HEAD is 829100068f68c12d75290b43af83c077cc482414

4 commits »

ggonnella pushed to assembly at ggonnella/genometools Fri Nov 13 00:33:56 -0800 2009

HEAD is 873da103ccb0e3a9eea8236948e23ff6004ca044

2 commits »

ggonnella pushed to assembly at ggonnella/genometools Thu Nov 12 10:24:25 -0800 2009

HEAD is 064af19c329e6184c3414bbb4dc18aac30166196

3 commits »

ggonnella pushed to assembly at ggonnella/genometools Thu Nov 12 08:47:37 -0800 2009

HEAD is a00ed5c67856fc401eabb12bd20c3945d9735dcd

16 commits »

ggonnella committed a00ed5c6:

apspm_pairwise (and corresp. tools) now use ovlfind_bf/dp
ggonnella committed 82da5624:

defined GtOvlproc[A] function ptr types
ggonnella committed 55015fd1:

ovlfind_dpmax improved (run _dp only once) and corrected
ggonnella committed 8ab21261:

ovlfind_dpmax unit tests
ggonnella committed 131e6248:

unit tests for ovlfind_bfmax
ggonnella committed e5ae1f33:

unit tests for ovlfind_dp module
ggonnella committed 7d1be278:

unit tests for ovlfind_bf module
ggonnella committed b465700f:

Ovl processor for unit tests
ggonnella committed 15e6a8f4:

corrected "old" overlap_show function; now comparison tests work
ggonnella committed 7de4099c:

ovlfind_bf/dp: modules to find with GT_OVLFIND_MAX breadth
ggonnella committed 258103c6:

ovlfind_bf/dp: allow unidirectional search
ggonnella committed 140f5f67:

ovl/ovl_a: allow some NULL params by read() and cmp()
ggonnella committed 82d54753:

GtOvlfindBreadth replaces GtApspmMaximality
ggonnella committed e5ae1293:

corrected definition of the ovl/ovl_a bools
ggonnella committed b0424392:

Enum defining the breadth of ovl search: all overlaps, "local" max, overall max
ggonnella committed 0fe970ea:

apspm testsuite: equivalent results with bf and esa in all cases

ggonnella pushed to assembly at ggonnella/genometools Tue Nov 10 10:26:32 -0800 2009

HEAD is 255881654c1ab1539263856fb4b09cc7a9b079c5

5 commits »

ggonnella pushed to assembly at ggonnella/genometools Tue Nov 10 08:13:17 -0800 2009

HEAD is 116480d08b6804ea68215d770cccc006b3ee0e39

28 commits »

ggonnella committed ab9f0508:

added in comment intended final interface for apspm_solver
ggonnella committed 592dcbba:

defined enumeration GtApspmMaximality
ggonnella committed f1469c5e:

Reorganisation of brute force overlap finder code
ggonnella committed 12bf4b17:

Reorganisation of dynamic programming overlap finder code
ggonnella committed aab7d63e:

apspm tool divided in 3 (apspm, apspm_bf, apspm_dp)
ggonnella committed 2f7e5453:

started reorganisation of apspm code
ggonnella committed c4f04019:

apspm tool, added new failing test case
ggonnella committed 513e4b65:

apspm esa: avoid double prefix-suffix and suffix-prefix results
ggonnella committed d64546d5:

apspm esa, implemented "remove contained reads" feature
ggonnella committed 2e6515eb:

apspm pairwise: remove contained reads also from previous results
ggonnella committed ac6685c6:

overlaps array methods moved to own files, show method added
ggonnella committed 59b22310:

overlap, added explicit containment status for equivalent reads
ggonnella committed 409b0c15:

bug fixed in esa-topdown-dfs
ggonnella committed d7022c6d:

apspm: found small failing test
ggonnella committed c16f5a2a:

apspm: replaced 12x800 testcase with 29x800 (max working correctly)
ggonnella committed c5718302:

Added own debug flags to Makefile
ggonnella committed 328968c0:

apspm test rewritten using -sort option; added new failing case
ggonnella committed ed65f899:

apspm esa: implemented options -sort and -f
ggonnella committed 53247685:

apspm_esa: option selfoverlap eliminated, some variables renamed
ggonnella committed f5a9c87d:

debug macros: move ifdef in header, use comment instead of (void)0

And 8 more commits...

ggonnella pushed to assembly at ggonnella/genometools Fri Oct 23 09:53:46 -0700 2009

HEAD is 99fcda80fac658c61b5da0446df62f550110c9d5

8 commits »

ggonnella committed 99fcda80:

apspm esa: implemented options -sort and -f
ggonnella committed 561f5af5:

apspm_esa: option selfoverlap eliminated, some variables renamed
ggonnella committed 8beec44e:

debug macros: move ifdef in header, use comment instead of (void)0
ggonnella committed 6cccf910:

test for the apspm tool
ggonnella committed 5c6f4d51:

fixed memleak in overlap.c
ggonnella committed d09167f9:

memory leak in overlap_line.c corrected
ggonnella committed e60cbc98:

Disabled strgr unit tests
ggonnella committed aba693f1:

fixed memleaks in GtOverlap unit test

ggonnella pushed to assembly at ggonnella/genometools Fri Oct 23 03:52:20 -0700 2009

HEAD is c3edece00f3c8345485e57662e957d6283d17b20

4 commits »

ggonnella pushed to assembly at ggonnella/genometools Fri Oct 23 02:53:41 -0700 2009

HEAD is c66a532a229a88842515aa68d89732825fda4278

11 commits »

ggonnella committed c66a532a:

most functions of determine_overlaps tool moved to apspm
ggonnella committed cc566d8a:

common code for apspm using db/bf collected in a module
ggonnella committed aa15e767:

GtOverlap, make use of gt_overlap_line functions
ggonnella committed 6d1828f3:

extended/apspm => apspm_esa
ggonnella committed c2457ad2:

overlap input/output function defining 2 file formats
ggonnella committed 1633c241:

apspm: allow to specify outfile
ggonnella committed 73a4c637:

apspm: minlen must be > 0
ggonnella committed fc3a8786:

moved debug macros of apspm.c in own file (and turned off)
ggonnella committed 0669b023:

esa topdown, debug macros moved to esa-topdown-dfs-debug.h
ggonnella committed 50a9fa11:

created "test" tool that traverses an esa lcp tree topdown
ggonnella committed a0ed8e7c:

output of overlap pretty print made similar to output of apspm module

ggonnella pushed to assembly at ggonnella/genometools Tue Oct 20 00:59:53 -0700 2009

HEAD is f67d8e848848bebce53a7a83b69b69b73b61dfa7

68 commits »

ggonnella committed 3ce13962:

implementation of string graph & tool to create a string graph from overlaps
ggonnella committed be4d0a1c:

tool for the determination of all overlaps of all fragments in the input file
ggonnella committed a85a9a6d:

simreads: improve -help messages
ggonnella committed e918af38:

simreads: added option to show progressbar
ggonnella committed 27bc3964:

simreads: better error handling in gt_simreads_runner()
ggonnella committed 0e739607:

simreads: added file options
ggonnella committed 128e8d1d:

simreads: added email for bug reports
ggonnella committed 7e96472c:

correct copyright year statement
Giorgio Gonnella committed a074d522:

simreads: removed some unused code lines
Giorgio Gonnella committed 3a61690a:

simreads: -coverage option alternative to -num
Giorgio Gonnella committed 9bb35d0d:

simreads: added -erate option to specify a read error rate
Giorgio Gonnella committed c1e38f35:

simreads: allow -maxlen to be equal to -minlen
Giorgio Gonnella committed 2f37f74b:

simreads tool: simulate sequencing reads from known sequences
Sascha Steinbiss committed 584b8d09:

do not compare integersize with reference
Sascha Steinbiss committed a5d6c588:

mgth: updates to manual text
Sascha Steinbiss committed da69dad1:

sort mgth statistics output
Sascha Steinbiss committed 56929ef6:

include error_api.h in dlist_api.h
Sascha Steinbiss committed 8df825fc:

Change mgth option giexpfilename from str_array to str
Sascha Steinbiss committed 2fe62247:

fix bug caused by wrong parameter order in assert
Sascha Steinbiss committed db1891dd:

add MetaGenomeThreader publication to webpage

And 48 more commits...

ggonnella pushed to master at ggonnella/genometools Tue Oct 20 00:59:52 -0700 2009

HEAD is 584b8d093c40da696086f0ba72d8c4ba598a3dd3

6 commits »

ggonnella pushed to assembly at ggonnella/genometools Fri Oct 16 04:20:19 -0700 2009

HEAD is fb5a52ea74c46c95c0b6cfb9d100f6e659442651

4 commits »

ggonnella pushed to master at ggonnella/genometools Fri Oct 16 04:20:19 -0700 2009

HEAD is db1891dd6df8ae61c0f533e4fbe57fa23bd45a7b

Sascha Steinbiss committed db1891dd:

add MetaGenomeThreader publication to webpage

ggonnella pushed to assembly at ggonnella/genometools Fri Oct 16 02:03:13 -0700 2009

HEAD is 77fd9c0514a1d732f4637b7b6b1bced28cb2e8f9

4 commits »

ggonnella pushed to assembly at ggonnella/genometools Thu Oct 15 04:34:45 -0700 2009

HEAD is d7624443c6c7b15005eb510547d9afe0faa0daad

ggonnella pushed to assembly at ggonnella/genometools Thu Oct 15 04:09:57 -0700 2009

HEAD is e9f3ac5c6ec64efce16ed4424efc8a4a1886c60a

107 commits »

Stefan Kurtz committed f17cdab3:

Added script to randomly select sequences from a file
Stefan Kurtz committed 4415059b:

Added program to split files.
Stefan Kurtz committed 49b2da71:

Added break.
Stefan Kurtz committed df198a3a:

renamed fasta2sequencekeyvalues into gt_inputfiles2sequencekeyvalues and add maximum sequence length constraint for 32bit.
Stefan Kurtz committed 6b039664:

Added option -showprogress: progressbar now must be used explicitely.
Stefan Kurtz committed 517b9dce:

Rename Mtime into Sfxprogress.
Stefan Kurtz committed 8f59f0d8:

Removed duplicated words in reference to tallymer paper.
Stefan Kurtz committed d88ecae2:

Add file to describe the symbol for Protein mass matching.
Stefan Kurtz committed 80e5a003:

Use larger maximum size for keys.
Stefan Kurtz committed c0b16dbc:

Generalized script to extract keys from fasta file.
Gordon Gremme committed 32f69eb8:

OPrval -> GtOPrval
Gordon Gremme committed 96e99981:

GTR -> GtR
Gordon Gremme committed 3fb770b9:

Merge branch 'master' of ssh://gordon@genometools.org/var/www/pub/git/genometools
Sascha Steinbiss committed 2c5b5219:

add HMMER external source dir to .gitignore
Sascha Steinbiss committed df097f2c:

gtpython: make GTError a subclass of RuntimeError
Sascha Steinbiss committed f173b547:

gtpython: make tracks sortable
Sascha Steinbiss committed 77c1bb89:

gtruby: allow track ordering
Sascha Steinbiss committed c08ab66c:

make track order sortable
Sascha Steinbiss committed 880a03d0:

mention LTRdigest publication on website
Gordon Gremme committed ed368d6c:

add gth_input_preprocess()

And 87 more commits...

ggonnella pushed to master at ggonnella/genometools Thu Oct 15 04:09:45 -0700 2009

HEAD is 1cd7df8c4ba104a345639b8dee4adddca7035b5e

45 commits »

Stefan Kurtz committed 49b70b5d:

Call function for palindromic matching.
Stefan Kurtz committed 9097a474:

Introduce Querysubstring into query matching algorithm.
Stefan Kurtz committed ca940ace:

Move the Queryrep structure from inside runquerysubstringmatch to the outside.
Stefan Kurtz committed fa716954:

Renamed mmsearchiterator into mmsearchiterator_plain
Stefan Kurtz committed b0baa8fd:

Now implemented rununque as an additional testcase.
Stefan Kurtz committed a16ae382:

Implemented calls to runmerge in the testsuite.
Stefan Kurtz committed 78422826:

The comparison of the prj files is now part of the testsuite.
Stefan Kurtz committed ffad590f:

Added reference prjfiles.
Stefan Kurtz committed c7d93408:

entangled loops calling cmpdbfile.sh and rununique.sh
Stefan Kurtz committed 6fef152f:

Replace call to mkvtree/vseqselect by ruby scripts.
Stefan Kurtz committed f17cdab3:

Added script to randomly select sequences from a file
Stefan Kurtz committed 4415059b:

Added program to split files.
Stefan Kurtz committed 49b2da71:

Added break.
Stefan Kurtz committed df198a3a:

renamed fasta2sequencekeyvalues into gt_inputfiles2sequencekeyvalues and add maximum sequence length constraint for 32bit.
Stefan Kurtz committed 6b039664:

Added option -showprogress: progressbar now must be used explicitely.
Stefan Kurtz committed 517b9dce:

Rename Mtime into Sfxprogress.
Stefan Kurtz committed 8f59f0d8:

Removed duplicated words in reference to tallymer paper.
Stefan Kurtz committed d88ecae2:

Add file to describe the symbol for Protein mass matching.
Stefan Kurtz committed 80e5a003:

Use larger maximum size for keys.
Stefan Kurtz committed c0b16dbc:

Generalized script to extract keys from fasta file.

And 25 more commits...

ggonnella pushed to master at ggonnella/genometools Sun Oct 11 10:08:12 -0700 2009

HEAD is 32f69eb88a701d3b0383807ab71ea0d4a271c637

10 commits »

Gordon Gremme committed 32f69eb8:

OPrval -> GtOPrval
Gordon Gremme committed 96e99981:

GTR -> GtR
Gordon Gremme committed 3fb770b9:

Merge branch 'master' of ssh://gordon@genometools.org/var/www/pub/git/genometools
Sascha Steinbiss committed 2c5b5219:

add HMMER external source dir to .gitignore
Sascha Steinbiss committed df097f2c:

gtpython: make GTError a subclass of RuntimeError
Sascha Steinbiss committed f173b547:

gtpython: make tracks sortable
Sascha Steinbiss committed 77c1bb89:

gtruby: allow track ordering
Sascha Steinbiss committed c08ab66c:

make track order sortable
Sascha Steinbiss committed 880a03d0:

mention LTRdigest publication on website
Gordon Gremme committed ed368d6c:

add gth_input_preprocess()

ggonnella (Giorgio Gonnella)

Following 1 githubber and watching 10 repositories view all →

Public Repositories (6)

genometools

ruby_progress_bar

active_scaffold_list_filters

genomeviewer

boxover_helper

attr_hidden

Public Activity