ModBase Todo List (Internal Todo List)
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Please send bug reports and/or suggestions/corrections to .
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Task
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Priority
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Status
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| Ligbase Sketch displays always the template residues, change to current residues |
0 |
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| Add Ligbase message ->no ligand found |
0 |
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| Change ligand display: summarize template and inheritance ligand binding residues |
1 |
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| Add specific SNP search page |
1 |
queued |
| Revisit model filter routine |
1 |
queued |
| Connect to PiBase' scop tables |
2 |
queued |
| Facilitate scop search |
2 |
queued |
| Make searches more flexible (whatever* vs. whatever, +,-,etc.) for all search categories |
2 |
queued |
| Add interacting proteins |
4 |
waiting for input tables |
| Add modbase tools (convert sequence/seq_id, collect database synonyms, etc) |
4 |
queued |
| automatically update PDB-code for nysgxrc datasets |
1 |
queued |
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| add todo list and add link to home page |
8/16/04 |
finished |
| read ucsf web-pages guidelines and check for compliance. |
8/17/04 |
finished |
| added ucsf compliant header and changed modbase header to fit |
8/17/04 |
finished |
| created general/authors/resources/etc. txt files in txt directory |
8/23/04 |
finished |
| populate content to links on home page (currently old info) |
8/23/04 |
finished |
| Loaded new trembl run (trembl2004), removed old runs, updated all tables for it |
10/14/04 |
done, bugfix pending |
| changed chimera call for new table structure |
10/15/04 |
done |
| create swissprot, uniprot and genome browser links (direct links to model_details page) |
1/19/05 |
done |
| automate keyword collection (internal table structure) |
1/19/05 |
done |
| Change chimera call to display LigBase and SNP residues in cpk |
1/20/05 |
done |
| Change links from Expasy and Genome Browser to go the modbase-new |
1/21/05 |
done |
| Added Chimera instructions and other entries to the help file |
1/21/05 |
done |
| Added Help links on Model Overview Page |
1/21/05 |
done |
| Added public nysgxrc datasets to public dataset (permission fix) |
1/22/05 |
done for modpipe_runs |
| Added external link construction for dataset_name |
1/25/05 |
done |
| Changed default displaymode to Model Overview for hand-selected Datasets |
1/25/05 |
done |
| Add Crosslink to dbali |
1/31/05 |
done |
| Fix model_details for too many models (hangs) |
1/31/05 |
enforced property for trembl datasets |
| select reasonable subset of models/sequences when no properties in input (to avoid runaway queries) |
1/31/05 |
see above |
| Add statistics page on home page (maybe, interactive) |
1/25/05 |
done, just copied from old pages |
| enabled filtering option for snpview and ligand view |
2/22/05 |
done |
| fixed image for LS-SNP and Genome Browser to display correct model |
2/22/05 |
done |
| check pdb link ->sometimes the wrong template shown |
3/2/5 |
done |
| Adjust Interface for ModPipe2 datasets |
2/25/5 |
done |
| Include models from unselected datasets in thumbprint table |
2/26/05 |
done |
| change scripts to accomodate modpipe2 structures |
2/22/5 |
done, revisit when E. changes modpipe2 to agreed structure |
| download and parse CATH flatfiles, display domain coverage |
3/3/5 |
done |
| Reorganized coordinate download: if only one model, don't add xml header, propagate seq_id for seqview,truncate at 300 models |
3/7/5 |
done |
| fix various LS-SNP connection bugs |
3/11/05 |
done |
| Include PDB in weekly updates |
3/11/05 |
done |
| Fix template bug for dataset snp-human2 |
3/28/05 |
done |
| Add retrieve script to retrieve all models or alignments for a databaseID |
4/18/05 |
done |
| automate ligbase updates |
5/23/05 |
done |
| automate inheritor updates |
5/23/05 |
done |
| import dataset from varsplic sequences, and new uniprot sequences |
6/1/05 |
done |
| import yeast dataset from ensembl sequences |
6/3/05 |
done |
| create links to ensembl yeast pages |
6/3/05 |
done |
| create links to ucsc genome browser for all their organims when match is found |
6/6/05 |
done |
| added news site to home page |
6/6/05 |
done |
