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File Rev. Age Author Last log entry
 Parent Directory        
SeedComponents/        
WebApplicationComponents/        
tests/        
ACH_resolution.cgi  1.13  11 years  olson  Changes for standalone use of this script.
AttribXMLRPC.cgi  1.9  12 years  parrello  Added support for the new method to get attribute descriptions by group.
Attributes.cgi  1.13  11 years  parrello  Fixed. Deprecated ScriptSetup methods are no longer exported by Tracer.
COPYING.TXT  1.1  13 years  olson  add license file
DocDirectory.cgi  1.7  13 years  parrello  Changed to use the new PageBuilder call signature.
Emergency.cgi  1.18  11 years  parrello  Made it harder for unauthorized people to invoke the script. The script only wor...
FigSQL.cgi  1.2  13 years  parrello  Fixed botched attempt to allow multi-table FIG queries.
FormDisplay.cgi  1.2  13 years  olson  add license words
HOPSS.cgi  1.8  13 years  olson  add license words
Makefile  1.18  12 years  parrello  Converted cp -p to cp to avoid a problem with makefiles.
ProcessTemplate.cgi  1.5  11 years  parrello  Fixed. Deprecated ScriptSetup methods are no longer exported by Tracer.
README  1.1.1.1  15 years  efrank   import
SearchSkeleton.cgi  1.29  11 years  parrello  Changed to hide the property search from the master list.
SeedComponents.pm  1.3  13 years  paczian  *** empty log message ***
SetPassword.cgi  1.11  11 years  parrello  Changed POD format for better compatability with Wiki.
ShowPage.cgi  1.2  13 years  olson  add license words
ShowTableFile.cgi  1.3  11 years  parrello  Fixed. Deprecated ScriptSetup methods are no longer exported by Tracer.
SimBlockDisplay.cgi  1.7  11 years  parrello  Fixed. Deprecated ScriptSetup methods are no longer exported by Tracer.
SimBlockForm.cgi  1.7  11 years  parrello  Fixed. Deprecated ScriptSetup methods are no longer exported by Tracer.
SimBlockPattern.cgi  1.8  11 years  parrello  Fixed. Deprecated ScriptSetup methods are no longer exported by Tracer.
SimPieces.cgi  1.5  11 years  parrello  Fixed. Deprecated ScriptSetup methods are no longer exported by Tracer.
SpanishInquisition.cgi  1.1  11 years  parrello  Created to test the Confess method.
WebApplicationComponents.pm  1.3  13 years  paczian  *** empty log message ***
add_links.cgi  1.2  13 years  olson  add license words
aliases_to_pubmed.cgi  1.8  12 years  hwang  Add in routines that save the attributes to ROLE_FROM_PEG_CURATED_RELEVANT
align_DNA.cgi  1.5  13 years  olson  add license words
array2sub.cgi  1.14  13 years  olson  add license words
assign_using_tree.cgi  1.16  11 years  disz  Display subsystems on hover
assignments.cgi  1.16  13 years  overbeek  add potentially_missed_assignments
att2sub.cgi  1.6  13 years  olson  add license words
bbhs.cgi  1.4  12 years  parrello  Changed so that the local datbase is opened if the current HTTP HOST is not a bi...
check_anno.cgi  1.2  13 years  overbeek  fix numbers on chedck_anno.cgi
check_bad.cgi  1.1  13 years  overbeek  add check_bad.cgi
check_fc.cgi  1.1  12 years  overbeek  add check_fc.cgi
check_int_anno.cgi  1.3  13 years  overbeek  $/ fixes
check_peg_functions.cgi  1.2  11 years  overbeek  add line numbers
check_subsys.cgi  1.26  12 years  overbeek  attempt to fix some of the mistakes introduced into check_subsys.cgi
check_variants.cgi  1.11  11 years  overbeek  allow different format for roles, rules and definitions in check_variants.cgi
chromosomal_clusters.cgi  1.113  11 years  parrello  Added tracing support.
chromosomal_clusters_old.cgi  1.2  13 years  parrello  Changed to use the new PageBuilder call signature.
close_genome_discrepancies.cgi  1.8  13 years  redwards  minor updates to ev code and default params
clust_ss.cgi  1.5  11 years  overbeek  fixes to the ACH_resolution stuff
cluster_service.cgi  1.4  13 years  olson  add license words
cluster_stage.cgi  1.4  13 years  olson  add license words
cluster_xmlrpc.cgi  1.2  13 years  olson  add license words
comp_MR.cgi  1.4  12 years  overbeek  fixed to comp_MR.cgi and FIGV.pm
comp_genomes.cgi  1.10  11 years  parrello  Added tracing support.
conflicted_pegs.cgi  1.2  13 years  olson  add license words
consistent_sets.cgi  1.3  13 years  olson  add license words
construct.cgi  1.3  13 years  olson  add license words
correspondence.cgi  1.2  13 years  olson  add license words
cv.cgi  1.16  13 years  olson  add license words
das.cgi  1.15  13 years  olson  add license words
diagram.cgi  1.8  11 years  parrello  Fixed a bug caused by an unspecified action parameter.
diagram_upload.cgi  1.2  12 years  paarmann  fixed the hrefs
diffsF.cgi  1.8  11 years  overbeek  change ::data/FigfamsData to ::FigfamsData
display_role_literature.cgi  1.4  12 years  hwang  Fix bug of 1 literature doesn't show up
display_subsys.cgi  1.29  11 years  parrello  Fixed to use new NMPDR mode protocol.
edit_feature.cgi  1.1  12 years  overbeek  initial, undebugged version of edit_feature.cgi
eggs.cgi  1.9  13 years  paczian  minor cosmetic changes to layout and text
extend_subsys.cgi  1.12  13 years  redwards  using is_environmental
feature.cgi  1.9  12 years  overbeek  fixes to allow non-peg features in subsystems
ff.cgi  1.2  12 years  overbeek  fix test for writable built in FigFam.pm
fid_checked.cgi  1.44  12 years  overbeek  fixes to display on protein page, alternative formats for alignments and trees i...
fig_scripts_service.cgi  1.10  11 years  redwards  more methods for metagenomes
figfam_proto.cgi  1.6  12 years  mkubal  added ss info
find_poss_subsys_instances.cgi  1.2  11 years  overbeek  fixes to find_poss_subsys_instances.cgi
find_reaction_paths.cgi  1.1  12 years  olson  Hope College modifications.
find_ss_genes.cgi  1.4  12 years  overbeek  added code to show connections between subsystems
frame.cgi  1.10  13 years  paczian  removed display of proteinpage due to new backend
fusions.cgi  1.2  13 years  olson  add license words
genome_statistics.cgi  1.54  12 years  parrello  Removed the contig display for Sprout.
genomebrowser.cgi  1.8  13 years  redwards  minor change to allow proper genome selection
get_expert_2c.cgi  1.7  11 years  overbeek  minor check for division by 0 in get_expert_2c.cgi
get_map_image.cgi  1.4  13 years  olson  add license words
header  1.1.1.1  15 years  efrank   import
heat_map.cgi  1.20  13 years  overbeek  RAE: minor changes to heat map interface
homologs_in_clusters.cgi  1.13  11 years  parrello  Changed to use FIG_CGI.
hope_tools.cgi  1.3  11 years  dejongh  Hope College updates
index.cgi  1.130  11 years  parrello  Added Etracing support.
install_subsystem_dir.cgi  1.1  12 years  olson  CGI for installing subsystem directory.
kernel.cgi  1.15  13 years  olson  add license words
kernel_xmlrpc.cgi  1.11  13 years  efrank   'by_raw_alias' => $wrapper->wrap_array_return("by_raw_alias"), 'fin...
legionella_v1.cgi  1.1  13 years  mkubal  tool for legionella ma analysis
legionella_v4.cgi  1.3  13 years  mkubal  links for nonsubsys reactions
ligands.cgi  1.2  11 years  parrello  Fixed. Deprecated ScriptSetup methods are no longer exported by Tracer.
link.cgi  1.6  11 years  parrello  Updated to direct users to the seed viewer.
list_subsys.cgi  1.1  13 years  olson  fixes
local_sim_compute.cgi  1.3  13 years  olson  more fixes to sim compute stuff.
locate_patterns.cgi  1.1  12 years  overbeek  add ability to filter aux roles on peg_to_subsystems
lock_subsys.cgi  1.2  12 years  overbeek  allow selection of all roles/genomes for locking
ma2sub.cgi  1.6  13 years  olson  add license words
ma_to_tf.cgi  1.4  12 years  mkubal  upgrade
ma_to_tf_nr.cgi  1.3  13 years  mkubal  with orpv
ma_to_tf_pairs.cgi  1.1  13 years  mkubal  with orpv
ma_to_tf_single.cgi  1.1  13 years  mkubal  new
makewsdl.pl  1.3  11 years  disz  Replaced after Rob delete
myseed.cgi  1.2  13 years  olson  add license words
nmpdr_aliases_to_pubmed.cgi  1.4  13 years  hwang  fix grammatical error
organisms.cgi  1.32  13 years  overbeek  RAE: Updating organisms.cgi for more information per organim
p2p_service.cgi  1.2  13 years  olson  add license words
paint_network.cgi  1.1  13 years  mkubal  for painting ma,flux results, complete genome hybridization exp
pathway.cgi  1.2  13 years  olson  add license words
pchs.cgi  1.4  11 years  olson  put the other batch coupling code in.
pir.cgi  1.33  13 years  olson  add license words
pom.cgi  1.22  12 years  overbeek  add check_variants.cgi, a program to automatically validate variant codes
propose_new_peg.cgi  1.11  13 years  golsen  Fix endpoint error when negative strand region runs off the start of the contig....
protein.cgi  1.250  11 years  parrello  Changed to redirect search engines to the seed viewer.
protein_by_ss.cgi  1.6  11 years  redwards  undoing horrible mistake
protein_info.cgi  1.10  13 years  olson  add license words
protein_new.cgi  1.6  13 years  parrello  Changed to use the new PageBuilder call signature.
protein_sets.cgi  1.4  13 years  olson  add license words
protein_sets_2.cgi  1.2  13 years  olson  add license words
protein_sets_by_alias.cgi  1.2  13 years  olson  add license words
proteinfamilies.cgi  1.47  13 years  overbeek  RAE: Changes to Protein Families
rae.cgi  1.4  13 years  olson  add license words
record.cgi  1.4  13 years  olson  add license words
region.cgi  1.1  12 years  paczian  initial version
reset_curator.cgi  1.4  13 years  overbeek  RAE: adding options to reset_curator
save_roles_to_attributes.cgi  1.1  12 years  hwang  Added files to display and show precomputed literature for functional roles with...
save_to_attributes.cgi  1.6  12 years  hwang  Add in routines that save the attributes to ROLE_FROM_PEG_CURATED_RELEVANT
scopmap_service.cgi  1.4  13 years  olson  add license words
sdk_uniprot_search.cgi  1.7  13 years  mkubal  Gene now Gene Name or Symbol
search_log.cgi  1.3  13 years  hwang   Change absolute path to relative path for getting genome log data
seed_ctl.cgi  1.13  11 years  olson  add ability to disable just the control panel.
seed_running_perl.fragment  1.2  13 years  olson  fixes
select.cgi  1.15  11 years  parrello  Added Etracing support.
server_check.cgi  1.3  13 years  olson  add license words
set_variants.cgi  1.5  13 years  overbeek  RAE: Adding a link into set variants from subsys.cgi and back
show_exp_assertions.cgi  1.9  11 years  overbeek  fix to show_exp_assertions.cgi
show_kegg_map.cgi  1.4  13 years  redwards  fixing broken links on map pages that refered fig ids to KEGG
show_local_map.cgi  1.5  13 years  redwards  fixing broken links on map pages that refered fig ids to KEGG
show_log.cgi  1.3  13 years  overbeek  add ability to log arbitrary correspondences
show_map.cgi  1.4  13 years  redwards  fixing broken links on map pages that refered fig ids to KEGG
sigs.cgi  1.52  11 years  parrello  Changed to use new NMPDR mode protocol.
split_functional_role.cgi  1.2  13 years  overbeek  to make sure
ss_correlations.cgi  1.4  12 years  overbeek  check sz of rep tree to 40 in insert_prot_into_tree
ss_export.cgi  1.8  13 years  olson  add license words
ss_scoreboard.cgi  1.9  13 years  olson  add license words
ssa.cgi  1.32  13 years  olson  add license words
ssa2.cgi  1.50  13 years  olson  add license words
start.cgi  1.10  13 years  overbeek  RAE: updated start interface
status_of_model.cgi  1.5  13 years  olson  add license words
subsys.cgi  1.214  11 years  overbeek  allow non-numeric variant codes
subsys_diagram.cgi  1.8  13 years  parrello  Fixed to work in Sprout.
subsys_hope.cgi  1.2  13 years  olson  add license words
subsys_summary.cgi  1.25  13 years  olson  add license words
subsys_vectors.cgi  1.13  13 years  overbeek  RAE: removing legacy static urls
targets.cgi  1.8  11 years  parrello  Fixed. Deprecated ScriptSetup methods are no longer exported by Tracer.
testGetControlledVocabularyAnnotationsForPegServer.cgi  1.1  13 years  efrank   server side for caBIG related regression tests.
testGetFigIdsForUniprotKbPrimaryAccessionServer.cgi  1.1  13 years  efrank   server side for caBIG related regression tests.
testGetFunctionalRolesByUniprotkbPrimaryAccessionServer.cgi  1.1  13 years  efrank   server side for caBIG related regression tests.
testGetGeneForPegServer.cgi  1.1  13 years  efrank   server side for caBIG related regression tests.
testGetOrganismCollectionServer.cgi  1.1  13 years  efrank   server side for caBIG related regression tests.
testGetOrganismsInSubsystemServer.cgi  1.1  13 years  efrank   server side for caBIG related regression tests.
testGetPegsForControlledVocabularyAnnotationServer.cgi  1.1  13 years  efrank   server side for caBIG related regression tests.
testGetPegsForEnsemblgeneIDServer.cgi  1.1  13 years  efrank   server side for caBIG related regression tests.
testGetPegsForOrganismServer.cgi  1.1  13 years  efrank   server side for caBIG related regression tests.
testGetPegsInNeighborhoodServer.cgi  1.1  13 years  efrank   server side for caBIG related regression tests.
testGetPegsInSubsystemCellServer.cgi  1.1  13 years  efrank   server side for caBIG related regression tests.
testGetSubsystemCollectionServer.cgi  1.1  13 years  efrank   server side for caBIG related regression tests.
testGetSubsystemsHavingOrganismServer.cgi  1.1  13 years  efrank   server side for caBIG related regression tests.
testGetUniprotKbPrimaryAccessionsForFigIdServer.cgi  1.1  13 years  efrank   server side for caBIG related regression tests.
test_basic_functionality.cgi  1.1  11 years  olson  basic func test - for nagios
tree_jnlp.cgi  1.2  11 years  disz  Fixed href error in the jnlp
tyra_cluster.cgi  1.1  12 years  hwang  given a tyra peg/ it finds the gene neighborhood of that peg
tyra_sequence.cgi  1.2  12 years  hwang  add modified sequences
users.cgi  1.2  13 years  olson  add license words
vert_text.cgi  1.2  13 years  olson  add license words
wiki.cgi  1.1  11 years  parrello  Added to allow for a short URL to get to the wiki.
wsdl.cgi  1.1  11 years  redwards  changing the makewsdl script to a live cgi

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