2020-07-31

• Server code updated to SLiMSuite v1.8.1 development code.
• New faster server should be coming soon. Hopefully with some bug fixes with walltimes etc.
• There have been some issue with jobs getting stuck in queues or hanging indefinitely after hitting the walltime. Fixes will be found once time allows. Please contact me if you get confused by job behaviour!

2019-05-23

• Default disorder predictor updated to IUPred2 (short mode)

2019-05-10

• Server code synced with SLiMSuite v1.8.0 pre-release on GitHub.
• NOTE: Server data is currently undergoing a major overhaul and refresh for a SLiMSuite protocols paper. Watch this space, and look out for changes in data.

2018-07-02

• Server code synced with SLiMSuite release v1.4.0 (2018-07-02) on GitHub.
• Bettong genome added to the WebApollo search server. This is password protected - please get in touch if you want access.

2018-06-14

• There was an issue with Uniprot retrieval after a change in behaviour by the Uniprot website. I am not sure when this occurred but it should now be fixed with v3.25.0 of rje_uniprot. The bug caused only the first entry of a list to be downloaded, resulting in multiple download failures. (Regrettably not in a fashion that triggered the alternative one-by-one download protocol. This can now be activated independently with onebyone=T.)

Further news

Please visit http://slimsuite.blogspot.com.au for additional (and older) news/updates.

2017

2017-12-19

• Underlying code updated to SLiMSuite release v1.3.0.

2017-10-30

• Added password protection for some input aliases for embargoed data access.
• Added developmental BLAST server.

2017-09-27

• Server code updated to latest SLiMSuite code. (This is newer than the current package but can be accessed via svn download of the development code.) The main servers have been tested but please report any unusual behaviour!
• New QSLiMFinder and SLiMProb servers have been added with simple input forms. This is still in development and needs additional documentation: please get in touch if you have any questions.

2017-04-03

• Server code updated to latest SLiMSuite code. (This is newer than the current package but can be accessed via svn download of the development code.) The main servers have been tested but please report any unusual behaviour!
• A new SLiMFinder server has been added with a simple input form. This is still in development and needs additional documentation: please get in touch if you have any questions.
• A FAQ page has been added: please get in touch if you have any questions!

2017-01-27

• Server code updated to latest SLiMSuite code. (This is newer than the current package but can be accessed via svn download of the development code.) The main servers have been tested but please report any unusual behaviour!
• SLiMProb now merges the results from "split" motifs in the main output. To revert this behaviour to the previous version, set mergesplits=F.
• The Uniprot server now outputs a map table that maps the entered list of IDs and accession numbers onto the primary accession numbers downloaded. This table is also output for SLiMProb and (Q)SLiMFinder.

2016

2016-09-08

• New SMRTSCAPE server to replace old PacBio server.
• Server code updated to latest SLiMSuite code. (This is newer than the current package but can be accessed via svn download of the development code.) The main servers have been tested but please report any unusual behaviour!

2016-08-23

• Added server queue limits. (Max 50 per IP address, max 500 total.) There is also a limit to how many jobs will be run in parallel for a given IP address. This currently corresponds to 3 "big" jobs (e.g. SLiMFinder) but many more small job.
• Added new REVERT genome aliases. Updated REVERT output.

2016-08-22

• Fixed SMRTScape output bug following coverage=F default setting switch.

2015

2015-12-07

• Updated SLiMFinder documentation and SLiMSuite warnings.

2015-11-30

• SLiMSuite code updated to v1.1.0, release 2015-11-30.

2015-06-19

• Temporary glitch in SLiMProb, SLiMFinder, QSLiMFinder and SLiMMaker servers has been fixed.

2015-06-17

• Updated Tools page with more REST services.
• Changed the disorder server to iuscore to avoid future conflicts with the rje_disorder module.
• Made some minor modifications to SLiMSuite command processing and defaults for compatibility with the SLiMScape Cytoscape App.

2015-06-04

• Added XRef server for database cross-referencing.

2015-06-03

• Added PPI datasets for seqin and uniprot aliases.
• Modified (Q)SLiMFinder defaults for server to cloudfix=T.

2015-05-28

• Added PacBio and SLiMMaker server forms.

2015-05-18

• Fixed issues with SLiMFinder and QSLiMFinder servers.
• Updated SLiMProb, SLiMFinder and QSLiMFinder servers for use with SLiMScape Cytoscape App.

2015-05-15

• Updated alias files for new (April 2015) data
  • Quest For Orthologues Eukaryota orthdb
  • Ensembl *.dna.toplevel.fa genome files
  • ELM motif database and individual ELM motifs

2015-01-31

• Added GOPHER to the REST servers.
• Updated alias files.

2015-01-30

• Alias file access no longer needs the alias: prefix to the option value, e.g. &seqin=alias:LIG_PCNA_PIPBox_1. Adding the prefix will enforce use as an alias and return an error if the alias is not found.
• Added documentation for alias settings, including return of contents, e.g. alias&seqin=LIG_PCNA_PIPBox_1.
• Maximum file sizes (10MB) have been implemented for server call returns. Please contact the administrator is this is too limiting.
• IP address tracking has been implemented. Each day, queues will preferentially run jobs for new users.
• SLiMFinder csv output renamed main.

2015-01-23

• Sequences can now be given directly to options such as seqin=FILE by using a list in the form: >name1:sequence1,>name2:sequence2,...>nameN,sequenceN. Note that the>characters preceding the first name is required for correct recognition. Names can contain addtional: characters but whitespace is not recommended and may not work.
• Alias file access now needs the alias: prefix to the option value, e.g. &seqin=alias:LIG_PCNA_PIPBox_1.

2015-01-22

• The underlying architecture has been tweaked, which should improve server stability.
• A new API system has been implemented. Please see the Programmatic access to SLiMSuite REST services page for more details.

2015-01-13

• New documentation options are now available. Program documentation can be accessed using docs&page=prog or prog&rest=docs.

2015-01-10

• SLiMMaker V1.3.0 : SLiMMaker now has a &varlength=T/F option [default=True], which will recognise indels in the provided peptides. If varlength=T, any gapped positions will be assessed based on the ungapped peptides at that position and a variable length inserted. This variable-length position may be a wildcard or it may be a defined position if there is sufficient signal in the peptides with amino acids at that position. If varlength=F then gapped positions will be ignored (treated as Xs) and variable length wildcards are not returned.

SLiMSuite REST services are currently under development. Please report any bugs or erratic behaviour.

Known Issues

• There have been some issue with jobs getting stuck in queues or hanging indefinitely after hitting the walltime. Fixes will be found once time allows. Please contact me if you get confused by job behaviour!
• Failing to provide required input options for servers is not currently robustly handled and may result in errors.
• Server errors may not be consistently returned in a fashion that is easy for an API to recognise.
• PeptCluster currently breaks if 2+ identical peptides are included in input.

• New faster server should be coming soon. Hopefully with some bug fixes with walltimes etc.
• Test PINGU server for extracted PPI data.

Please contact richard.edwards@unsw.edu.au for update requests.