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

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