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File Rev. Age Author Last log entry
 Parent Directory        
SeedComponents/        
WebApplicationComponents/        
tests/        
rast_save_sim_output.cgi  1.1  5 months  olson  New support for submitting sims to the Slurm cluster.
subsystem_server.cgi  1.10  20 months  olson  Add routine to return functional role table.
wc.cgi  1.19  4 years  olson  Add change from Ross's code.
genome_object.cgi  1.4  4 years  olson  Fix JSON encoding.
ss_directed_compare_regions.cgi  1.5  4 years  olson  link to ss editor, fix title
families_on_tree.cgi  1.4  5 years  overbeek  allow painting of multiple families
samples.cgi  1.5  5 years  overbeek  progress
study.cgi  1.1  5 years  overbeek  progress
stimulus.cgi  1.3  5 years  overbeek  add ar-names
peg.cgi  1.5  5 years  overbeek  add ar-names
atomic_regulon.cgi  1.4  5 years  overbeek  add ar-names
index.cgi  1.155  5 years  golsen  Major modifications to the blast interface. Use BlastInterface::blast() througho...
comp_genomes.cgi  1.12  6 years  golsen  Add a test on modification dates to force an update of the cached data.
rest_seed.cgi  1.3  6 years  redwards  correcting url encoding and empty url response
subsys.cgi  1.218  6 years  redwards  adding a column for the number of genomes associated with each role
rest_rtmg.cgi  1.3  6 years  redwards  more real time metagenomies
RTMg.cgi  1.7  6 years  redwards  adding RTMg pages
set_variants.cgi  1.6  6 years  redwards  adding a limitation to the set variants page
rast_submit_server.cgi  1.14  6 years  olson  Just use YAML::XS for parsing large documents.
seed_svc.cgi  1.2  6 years  olson  fix the cgi for seed svc
seed.psgi  1.1  6 years  olson  SEED service interface
Makefile  1.23  6 years  olson  SEED service interface
sap_server.psgi  1.1  6 years  olson  PSGI version of sap_server
exclude_from_solid_rectangles.cgi  1.1  6 years  overbeek  support excluding pegs from SR machinery
chromosomal_clusters.cgi  1.120  6 years  golsen  Attempt to fix problems with global variables and many structural issues. Deal w...
propose_new_peg.cgi  1.18  6 years  golsen  Update complete genome blast.
display_role_literature.cgi  1.6  6 years  golsen  Missed the key change. Fixed it now I hope.
protein.cgi  1.255  6 years  golsen  Try to suppress warning about redefining main(). This might only exist in FASTCG...
fid_checked.cgi  1.63  6 years  golsen  Order sequences in alignment to match the corresponding tree.
feature.cgi  1.11  6 years  golsen  Very large number of changes in link urls to work around problems with $cgi->url...
check_sets.cgi  1.3  6 years  overbeek  check for real fids
ar_coexp.cgi  1.8  7 years  overbeek  minor fix
display_subsys.cgi  1.31  7 years  golsen  Get rid of error log message for missing ec2go file.
ErdbDocWidget.cgi  1.5  7 years  parrello  Support for CDMI as a special type of ERDB database.
serv_genome.cgi  1.5  7 years  overbeek  mods suggested by Bob
serv_feature.cgi  1.7  7 years  overbeek  mods suggested by Bob
serv_otu.cgi  1.4  7 years  overbeek  mods suggested by Bob
serv_role.cgi  1.5  7 years  overbeek  mods suggested by Bob
serv_complex.cgi  1.5  7 years  overbeek  mods suggested by Bob
serv_reaction.cgi  1.5  7 years  overbeek  mods suggested by Bob
serv_FIGfam.cgi  1.5  7 years  overbeek  mods suggested by Bob
serv_subsysRow.cgi  1.6  7 years  overbeek  mods suggested by Bob
serv_index.cgi  1.2  7 years  overbeek  mods suggested by Bob
align_and_tree.cgi  1.6  7 years  golsen  Fix issue with user name under the SEED.
blank_svp.cgi  1.1  8 years  olson  Script & infrastructure for creating easy seedviewer pages.
MSSeedSupport_server.cgi  1.1  8 years  chenry  *** empty log message ***
FBAMODEL_server.cgi  1.4  8 years  chenry  *** empty log message ***
ErdbDbdPrint.cgi  1.1  8 years  parrello  Fix to ERDB documentation page.
anno_server.cgi  1.17  8 years  olson  Move inline code out of anno_server.cgi to ANNO.pm (well the code was already mo...
ssp2ss.cgi  1.1  8 years  overbeek  convert requests to subsystems
ssp.cgi  1.3  8 years  olson  Changes to seedviewerify the primer
resolve_paralogs.cgi  1.14  8 years  golsen  Add fraction identity filter for paralogs. Improve handling of links to the prot...
eggs.cgi  1.11  8 years  parrello  More fixes for Sveta
sigs.cgi  1.53  8 years  olson  fix links for seedviwer
FIG_Config.cgi  1.1  8 years  devoid  Adding FIG_Config.cgi a cgi-script that produces a javascript document that cont...
ModelImport_server.cgi  1.1  8 years  devoid  Ugg I can't remember them all!!!
alitre_server.cgi  1.1  8 years  parrello  New alignment/tree server stuff.
ncbi.cgi  1.1  8 years  olson  Ajax processor for upload ncbi lookups.
neighbor_tree.cgi  1.1  9 years  redwards  A web page to make trees
diffsF.cgi  1.9  9 years  disz  FigFam 6 digit problem
sup_server.cgi  1.1  9 years  parrello  New sapling update server script.
AT_server.cgi  1.1  9 years  fangfang  Initial import of alignment and tree server CGI
ma.cgi  1.12  9 years  overbeek  saving recent changes - it is still work in progress
webservices_seed.cgi  1.8  9 years  redwards  Changing FigFams/FigFam to FFs/FF
webservices_nmpdr.cgi  1.2  9 years  redwards  Changing FigFams/FigFam to FFs/FF
show_cffs.cgi  1.1  9 years  overbeek  show coupling between two FIGfams
staph_exp.cgi  1.1  9 years  overbeek  supports just Staph expression analysis
show_pegs.cgi  1.2  9 years  olson  fixe
graph_exp.cgi  1.1  9 years  olson  expression data grapher
figfam_server_2.cgi  1.23  9 years  olson  Push down default max requests.
ShowPod.cgi  1.4  9 years  parrello  Added module name to the output page title.
sgv.cgi  1.9  9 years  parrello  Fixed temporary directory setup for Genographics. Changed seed viewer URL comput...
check_role_in_ss.cgi  1.20  9 years  overbeek  Marks stuff
sap_server.cgi  1.3  9 years  parrello  Removed obsolete POD URL. Fixed the comments.
rssv.cgi  1.5  9 years  overbeek  a basic genome directory viewer
MODEL_server.cgi  1.1  9 years  chenry  *** empty log message ***
ach_server.cgi  1.8  10 years  parrello  Converted to new technology.
fabric.cgi  1.1  10 years  overbeek  explore differences in functional fabric
split_role_in_ss.cgi  1.4  10 years  overbeek  minor fixes
co_occurs_server.cgi  1.8  10 years  parrello  Removed a redundant "use".
MetagenomesByOrganism.cgi  1.1  10 years  redwards  new cgi for getting data
ribosomal_rnas.cgi  1.1  10 years  redwards  new cgi for getting data
webservices_rast.cgi  1.2  10 years  redwards  updated web services
webservices_mgrast.cgi  1.3  10 years  redwards  updated web services
subsystem_server_sapling.cgi  1.10  10 years  parrello  Converted to new technology.
get_dlits.cgi  1.13  10 years  overbeek  get rid of one-time code
WS_MGRAST.pm  1.1  10 years  jared  inital version
figfam_server_1.cgi  1.2  10 years  disz  fixed some error handling
figfam_server.cgi  1.1  10 years  disz  Simple version of figfam server
diagram.cgi  1.9  10 years  parrello  Changed to load the default styles.
wsdl_seed_complex.cgi  1.1  10 years  redwards  adding new ws with complex data types and accurate (ish?) data descriptions
RandomTest.cgi  1.2  10 years  parrello  Made even more random.
Emergency.cgi  1.23  10 years  parrello  Added support for alternate tracing keys for command-line tracing.
webservices_ACH.cgi  1.1  10 years  disz  New web services for ACH
wsdl_ach.cgi  1.1  10 years  disz  New wsdl for ACH web service
ex_assertions.cgi  1.11  10 years  overbeek  add check for cluster-based
WarnTest.cgi  1.1  10 years  parrello  Utility to test the RSS feed.
cleanup.cgi  1.4  10 years  overbeek  add sizes to tables
bad_roles.cgi  1.1  10 years  overbeek  check for lack of similarity within each column of an ss
aliases_to_pubmed.cgi  1.9  11 years  wilke  removed exit statement. Script proceeds now even if no ids are submitted.
hope_tools.cgi  1.4  11 years  dejongh  efficiency improvements
homologs_in_clusters.cgi  1.14  11 years  parrello  Redirected to evidence page if called from NMPDR.
check_ann_errs.cgi  1.3  11 years  overbeek  add target to links in check_ann_err.cgi
genome_statistics.cgi  1.56  11 years  parrello  Changed to use the SEED Viewer if invoked in NMPDR mode.
targets.cgi  1.9  11 years  parrello  Converted to work correctly with the wiki.
SearchSkeleton.cgi  1.31  11 years  parrello  Converted to work correctly with the wiki.
edit_feature.cgi  1.2  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
extend_subsys.cgi  1.13  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
assign_using_tree.cgi  1.17  11 years  golsen  Move writing of assignment annotation from a case-by-case basis (and it was miss...
Attributes.cgi  1.14  11 years  parrello  Changed to point to new attribute editor.
proteinfamilies.cgi  1.48  11 years  arodri7  redirect to new FIGfam page
ACH_resolution.cgi  1.14  11 years  overbeek  format display of comments to be surrounded by <pre>
get_dlit.cgi  1.5  11 years  overbeek  turn off old get_dlit.cgi
genome_feature_dna.cgi  1.1  11 years  golsen  Add the ability to get DNA sequences for all features of a given type in a genom...
wsdl_nmpdr.cgi  1.1  11 years  redwards  nmpdr web services version
fig_scripts_service.cgi  1.14  11 years  dsouza  pinned_regions_data modified to enable collapse_close_genomes
wsdl_seed.cgi  1.1  11 years  redwards  Adding new wsdl/web service components
wsdl_rast.cgi  1.1  11 years  redwards  Adding new wsdl/web service components
wsdl_mgrast.cgi  1.1  11 years  redwards  Adding new wsdl/web service components
display_subsystem_literature.cgi  1.1  11 years  wilke  similar to display_role_literature
SpanishInquisition.cgi  1.2  11 years  parrello  Added the "warn" parameter, which activates tracing before generating the error....
SimPieces.cgi  1.5  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.
SimBlockDisplay.cgi  1.7  11 years  parrello  Fixed. Deprecated ScriptSetup methods are no longer exported by Tracer.
ShowTableFile.cgi  1.3  11 years  parrello  Fixed. Deprecated ScriptSetup methods are no longer exported by Tracer.
select.cgi  1.15  11 years  parrello  Added Etracing support.
ligands.cgi  1.2  11 years  parrello  Fixed. Deprecated ScriptSetup methods are no longer exported by Tracer.
ProcessTemplate.cgi  1.5  11 years  parrello  Fixed. Deprecated ScriptSetup methods are no longer exported by Tracer.
check_peg_functions.cgi  1.2  11 years  overbeek  add line numbers
clust_ss.cgi  1.5  11 years  overbeek  fixes to the ACH_resolution stuff
tree_jnlp.cgi  1.2  11 years  disz  Fixed href error in the jnlp
check_variants.cgi  1.11  11 years  overbeek  allow different format for roles, rules and definitions in check_variants.cgi
show_exp_assertions.cgi  1.9  11 years  overbeek  fix to show_exp_assertions.cgi
wiki.cgi  1.1  11 years  parrello  Added to allow for a short URL to get to the wiki.
link.cgi  1.6  11 years  parrello  Updated to direct users to the seed viewer.
pchs.cgi  1.4  11 years  olson  put the other batch coupling code in.
get_expert_2c.cgi  1.7  11 years  overbeek  minor check for division by 0 in get_expert_2c.cgi
SetPassword.cgi  1.11  11 years  parrello  Changed POD format for better compatability with Wiki.
find_poss_subsys_instances.cgi  1.2  12 years  overbeek  fixes to find_poss_subsys_instances.cgi
test_basic_functionality.cgi  1.1  12 years  olson  basic func test - for nagios
makewsdl.pl  1.3  12 years  disz  Replaced after Rob delete
seed_ctl.cgi  1.13  12 years  olson  add ability to disable just the control panel.
protein_by_ss.cgi  1.6  12 years  redwards  undoing horrible mistake
wsdl.cgi  1.1  12 years  redwards  changing the makewsdl script to a live cgi
pom.cgi  1.22  12 years  overbeek  add check_variants.cgi, a program to automatically validate variant codes
check_fc.cgi  1.1  12 years  overbeek  add check_fc.cgi
check_subsys.cgi  1.26  12 years  overbeek  attempt to fix some of the mistakes introduced into check_subsys.cgi
region.cgi  1.1  12 years  paczian  initial version
locate_patterns.cgi  1.1  12 years  overbeek  add ability to filter aux roles on peg_to_subsystems
figfam_proto.cgi  1.6  12 years  mkubal  added ss info
install_subsystem_dir.cgi  1.1  12 years  olson  CGI for installing subsystem directory.
ff.cgi  1.2  12 years  overbeek  fix test for writable built in FigFam.pm
find_reaction_paths.cgi  1.1  12 years  olson  Hope College modifications.
AttribXMLRPC.cgi  1.9  12 years  parrello  Added support for the new method to get attribute descriptions by group.
comp_MR.cgi  1.4  12 years  overbeek  fixed to comp_MR.cgi and FIGV.pm
save_to_attributes.cgi  1.6  12 years  hwang  Add in routines that save the attributes to ROLE_FROM_PEG_CURATED_RELEVANT
save_roles_to_attributes.cgi  1.1  12 years  hwang  Added files to display and show precomputed literature for functional roles with...
diagram_upload.cgi  1.2  12 years  paarmann  fixed the hrefs
ma_to_tf.cgi  1.4  12 years  mkubal  upgrade
lock_subsys.cgi  1.2  12 years  overbeek  allow selection of all roles/genomes for locking
ss_correlations.cgi  1.4  12 years  overbeek  check sz of rep tree to 40 in insert_prot_into_tree
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
bbhs.cgi  1.4  12 years  parrello  Changed so that the local datbase is opened if the current HTTP HOST is not a bi...
find_ss_genes.cgi  1.4  13 years  overbeek  added code to show connections between subsystems
genomebrowser.cgi  1.8  13 years  redwards  minor change to allow proper genome selection
subsys_diagram.cgi  1.8  13 years  parrello  Fixed to work in Sprout.
WebApplicationComponents.pm  1.3  13 years  paczian  *** empty log message ***
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_map.cgi  1.4  13 years  redwards  fixing broken links on map pages that refered fig ids to KEGG
close_genome_discrepancies.cgi  1.8  13 years  redwards  minor updates to ev code and default params
nmpdr_aliases_to_pubmed.cgi  1.4  13 years  hwang  fix grammatical error
subsys_vectors.cgi  1.13  13 years  overbeek  RAE: removing legacy static urls
assignments.cgi  1.16  13 years  overbeek  add potentially_missed_assignments
frame.cgi  1.10  13 years  paczian  removed display of proteinpage due to new backend
seed_running_perl.fragment  1.2  13 years  olson  fixes
list_subsys.cgi  1.1  13 years  olson  fixes
DocDirectory.cgi  1.7  13 years  parrello  Changed to use the new PageBuilder call signature.
chromosomal_clusters_old.cgi  1.2  13 years  parrello  Changed to use the new PageBuilder call signature.
FigSQL.cgi  1.2  13 years  parrello  Fixed botched attempt to allow multi-table FIG queries.
check_bad.cgi  1.1  13 years  overbeek  add check_bad.cgi
start.cgi  1.10  13 years  overbeek  RAE: updated start interface
heat_map.cgi  1.20  13 years  overbeek  RAE: minor changes to heat map interface
reset_curator.cgi  1.4  13 years  overbeek  RAE: adding options to reset_curator
search_log.cgi  1.3  13 years  hwang   Change absolute path to relative path for getting genome log data
show_log.cgi  1.3  13 years  overbeek  add ability to log arbitrary correspondences
split_functional_role.cgi  1.2  13 years  overbeek  to make sure
SeedComponents.pm  1.3  13 years  paczian  *** empty log message ***
sdk_uniprot_search.cgi  1.7  13 years  mkubal  Gene now Gene Name or Symbol
organisms.cgi  1.32  13 years  overbeek  RAE: Updating organisms.cgi for more information per organim
legionella_v4.cgi  1.3  13 years  mkubal  links for nonsubsys reactions
ma_to_tf_pairs.cgi  1.1  13 years  mkubal  with orpv
ma_to_tf_nr.cgi  1.3  13 years  mkubal  with orpv
testGetPegsForEnsemblgeneIDServer.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.
testGetPegsForOrganismServer.cgi  1.1  13 years  efrank   server side for caBIG related regression tests.
testGetControlledVocabularyAnnotationsForPegServer.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.
testGetSubsystemCollectionServer.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.
testGetPegsInNeighborhoodServer.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.
testGetOrganismsInSubsystemServer.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.
testGetPegsForControlledVocabularyAnnotationServer.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.
testGetOrganismCollectionServer.cgi  1.1  13 years  efrank   server side for caBIG related regression tests.
check_int_anno.cgi  1.3  13 years  overbeek  $/ fixes
legionella_v1.cgi  1.1  13 years  mkubal  tool for legionella ma analysis
check_anno.cgi  1.2  13 years  overbeek  fix numbers on chedck_anno.cgi
local_sim_compute.cgi  1.3  13 years  olson  more fixes to sim compute stuff.
ma_to_tf_single.cgi  1.1  13 years  mkubal  new
kernel_xmlrpc.cgi  1.11  13 years  efrank   'by_raw_alias' => $wrapper->wrap_array_return("by_raw_alias"), 'fin...
paint_network.cgi  1.1  13 years  mkubal  for painting ma,flux results, complete genome hybridization exp
COPYING.TXT  1.1  13 years  olson  add license file
protein_info.cgi  1.10  13 years  olson  add license words
ma2sub.cgi  1.6  13 years  olson  add license words
conflicted_pegs.cgi  1.2  13 years  olson  add license words
users.cgi  1.2  13 years  olson  add license words
ssa.cgi  1.32  13 years  olson  add license words
subsys_hope.cgi  1.2  13 years  olson  add license words
das.cgi  1.15  13 years  olson  add license words
subsys_summary.cgi  1.25  13 years  olson  add license words
ss_scoreboard.cgi  1.9  13 years  olson  add license words
pir.cgi  1.33  13 years  olson  add license words
myseed.cgi  1.2  13 years  olson  add license words
fusions.cgi  1.2  13 years  olson  add license words
ss_export.cgi  1.8  13 years  olson  add license words
vert_text.cgi  1.2  13 years  olson  add license words
pathway.cgi  1.2  13 years  olson  add license words
get_map_image.cgi  1.4  13 years  olson  add license words
protein_sets_2.cgi  1.2  13 years  olson  add license words
correspondence.cgi  1.2  13 years  olson  add license words
ssa2.cgi  1.50  13 years  olson  add license words
cv.cgi  1.16  13 years  olson  add license words
server_check.cgi  1.3  13 years  olson  add license words
scopmap_service.cgi  1.4  13 years  olson  add license words
kernel.cgi  1.15  13 years  olson  add license words
status_of_model.cgi  1.5  13 years  olson  add license words
protein_sets_by_alias.cgi  1.2  13 years  olson  add license words
record.cgi  1.4  13 years  olson  add license words
rae.cgi  1.4  13 years  olson  add license words
protein_sets.cgi  1.4  13 years  olson  add license words
consistent_sets.cgi  1.3  13 years  olson  add license words
p2p_service.cgi  1.2  13 years  olson  add license words
construct.cgi  1.3  13 years  olson  add license words
cluster_xmlrpc.cgi  1.2  13 years  olson  add license words
array2sub.cgi  1.14  13 years  olson  add license words
FormDisplay.cgi  1.2  13 years  olson  add license words
align_DNA.cgi  1.5  13 years  olson  add license words
att2sub.cgi  1.6  13 years  olson  add license words
HOPSS.cgi  1.8  13 years  olson  add license words
ShowPage.cgi  1.2  13 years  olson  add license words
cluster_stage.cgi  1.4  13 years  olson  add license words
cluster_service.cgi  1.4  13 years  olson  add license words
header  1.1.1.1  15 years  efrank   import
README  1.1.1.1  15 years  efrank   import

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