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• MIAMExpress MIAMExpress7.5 file released: miamexpressaR7.5.tar.gz

  R7.5: ======= New Features: ------------- - Label used captured at labeled extract stage and displayed on hybridization page. New Checks: ----------- Bug Fixes: ---------- R7.3: ======= New Features: ------------- - Experiment design types split and related to experimental factors. - New experimental factors: ecotype, clinical information, ChIP-antibody, irradiation, individual. - More descriptive final submission emails - flagging batch upload emails, platform for first hyb, etc. New Checks: ----------- Bug Fixes: ---------- - exporting AGE as factor value when the unit is weeks. R2.0.1: ======= New Features: ------------- - New control vocabulary for experiment types. - New user definable protocol accession name in mage-ml. - Deletion of linked protocols changed - any linked protocol cannot be deleted. - Publication and authors pages combined under experimental design page. - MAGE-ML code change to how release date, submission date and display name are shown as NVTs now. - Species added to array design. New Checks: ----------- - Javascript warning on unlinked growth and treatment protocols. Bug Fixes: ---------- - Fix of control vocabulary Used Label typo. - Experimental factor value propagation from experimental design page. R2.0: ===== New Features: ------------- - Experiment graph visualization and navigation. - Public standard protocols. - Experimental Factor Values. - Compressed file uploading allowed now. - Normalization and Transformation protocols. [DONE IN PROD] - New control vocabulary. 6 new species. 50 new journals. 2 new sexes. 1 new Sample Type. 2 new Genetic Modifications. [DONE IN PROD] - Removal of control vocabulary. Sample Type: biopsy, blood, faeces. - Rearranging display order of control vocabulary. Label Used. - Unselect link for protocol binding. - Change to email subject line - shorter version preferred for curators. [DONE IN PROD] - New CV for publication status "submitted". [DONE IN PROD] - Submission (array and experiment) name length changed to 255 characters. [DONE IN PROD] - Creating backup copies of files removed by curators. - New and updated context-sensitive help popups and main help files. [DONE IN PROD] - Showing the help web page after signing up. - Parsing out javascript comments for faster web page construction. - On the Create Hybridizations page, having the labeled extracts as two separate drop down boxes. - HTML anchors set up from Hybridization page back to Create Hybridizations page. - Release drop down limited to 2005/2006. - Removed javascript message submitted successfully. - Removed SampleType as mandatory. - Removed Serial Number as mandatory. - Array design submission shows local protocols only. - Form changes javascript message changed to be shorter in length. - Add and migrate new publication statuses. - Add and migrate new separation techniques. - Add and migrate new hardware and software CVs. - Add and migrate new age time point, experiment type, scanning protocol, array attachment, array platform CVs. - Species cultivar change for Oryza sativa. - New field Strain on sample page. - Accession number association to MIAMExpress experiments and arrays. - Creating new table indexes and logging off feature to improve performance. - More interface text to aid submissions. - Better and shorter javascript error messages. New Checks: ----------- 1- Checks for Affy file uploads - CHP,EXP, etc. 2- Check protocol with data file (normalization and transformation). 3- Check for at least one hybridization in an experiment submission. 4- Check for author affiliation. Needed in MAGE creation. 5- Check for forward or backward slashes in submission names. 6- Check for spaces in login name. [DONE IN PROD] 7- Check for duplicate submission names (array and experiment). Required for curator running of MAGE-ML scripts. 8- Check for changes in author's page before navigating away. [DONE IN PROD] 9- Check for hold date made more flexible for different users. 10- Check for pooling protocol if more than one sample is submitted for an extract. 11- Check for filed in sample form before navigating to extract. 12- Check to stop a form from submitting when enter is pressed except in textarea or submit button. 13- Checks for suitable names for entities - including uploaded file names. Bug Fixes: ---------- 1- Final experiment submission page had a bug when uploading a file. To do with a hidden field which was not checked for existence. [DONE IN PROD] 2- File upload changed to first write to disk and then to database. Avoids browser timeout errors. [DONE IN PROD] 3- Paste across for label extracts changed all the label extracts to associated to one extract. Fixed now. [DONE IN PROD] 4- Login name and password changed to length of 16. MySQL limit of 16 characters for these. [DONE IN PROD] 5- Curator upload and removal of files wasn't possible before since login name was curator's and not original submitters. [DONE IN PROD] 6- Array protocol creating in array submission page bug. Can't return to array as array wasn't submitted to database. 7- Navigating from the quality related page back to the experiment page failed. Fixed now. [DONE IN PROD] 8- Paste across for hybridizations changes also array id, array batch and serial number which are not expected. Fixed now. [DONE IN PROD] 9- Organism name change from Brachidanio rerio to Danio rerio. 10- Sorting out bug from error report for labeled extract regarding extract navigation. R1.7-R1.9: ========== These were patches for getting better mage-ml: magexpress and db. R1.6: ===== New Features: ------------- This release was designed quickly to fix some small pending issues before the next major release. 1- Installation instructions updated. 2- Include magexpresspatch1.5.2 without having to download separately. 3- Updated context-sensitive Help Files (but not ADF, please refer still to http://www.ebi.ac.uk/~rocca/ADF/ADF_Help_v2.htm) 4- New control vocabularies: 4 species, 3 journals, 1 array. 5- Updated/removed CVs for post-transcriptional gene silencing, PLATFORM_TYPE, PREV_SAMPLE_TYPE, TREATMENT_VIVIVITRO, journal names changed, SCANNING_LABORATORY_PROTOCOL, SAMPLE_TYPE. Bug Fixes: ---------- 1- Fixes the function MX_HeavyInitialize function in MX_init.pm file. Caused by a differences in OS + Architecture. R1.5: ===== New Features: ------------- 1- Closing of the pending array and experiment submissions. 2- Curator (super-user) login feature. 3- ArrayExpress arrays can now be displayed and used directly from MIAMExpress. 4- Multiple File Upload for hybridization's raw and normalized data files, array design format (ADF) file and combined data file. 5- Array protocol is a standard protocol that could be referenced once it has been created. 6- Public release hold date for experiment and array submissions. 7- Adding hold date and more details to emails sent to submitters and curators. 8- New Pooling Protocol is a standard protocol that could be referenced once it has been created. 9- Changing Sample Cell Type to Sample Type. 10- Creating a quantitation type table for MAGE-ML parsing. 11- Cy3 and Cy5 checking at the hybridization level. 12- Adding an array accession number field for new array designs during experiment MAGE-ML creation. 13- New controlled vocabularies for experiment type, quality control steps, label used, sex, extracted product, array platform, and many more. 14- New help files for data files, Affymetrix submissions and FAQ. 15- More detailed installation help file. 16- Changing genetic variation to genetic modification. 17- Getting rid of animal from Strain label. 18- Direct navigation from experiment to create extracts and hybridization pages. Navigation is made more independent as well. Possible to navigate to any page from any page. 19- Paste across all entities functionality for samples, extracts, label extracts and hybridizations. 20- Migration script to migrate data from release 1.01 to 1.5. Bug Fixes: ---------- 1- Checking for samples associated with extracts before editing an extract's details. 2- Showing an error message for the view description of protocols when nothing is selected for viewing. 3- Fixing Netscape 4.75 bug when viewing Browse Array Design Page. 4- Fixing an extract creation bug when directly navigating from the Experiment page to Create Extracts page. 5- Disconnecting from database handles properly. R1.01: ====== New Features: --------------- 1- Sample treatment protocol is a standard protocol that could be referenced once it has been created. 2- Growth condition protocol is a standard protocol that could be referenced once it has been created. 3- Feature mapping for GenePix data files for submissions which are based on ADF submitted array designs. 4- Pooling functionality; one can create an extract pooled from multiple sample. Other Changes and Bug Fixes: ---------------------------- 1- Unlike the previous version it generates email to the mailing list when a submitter sends a new array design. 2- The array design MAGE-ML creation program to write down the MAGE-ML file in the specified directory. 3- MAGE-ML creation program now creates external data files with the same name that submitter has submitted. 4- MAGE-ML creation program which creates MAGE-ML from ADF, now counts identifiers from 1 not 0. 5- Not creating two different compounds identifier for the same compound. 6- Growth condition duration: if submitter doesn't specify the time we shouldn't parse out the time unit. 7- Adding the not applicable to Time point drop down list. 8- Parse out the address in MAGE-ML file as organization's address. 9- Including Reporter Group in ADF parsed mage-ml file. 10-Take the Array design info from TARDESIN table and incorporate their values in the produced MAGE-ML file. 11-Add another OntologyEntry object and associated it as PolymerType in ADF->MAGE-ML creation. 12-MAGExpress doesnt create Database and DatabaseEntry objects when the values are NULL,anymore. 13-Having Submitter Role to the Person Object when ADF-> MAGE-ML. 14-Having Hardware and Software not as parameters of protocols but as hardware and software in MAGE-ML file. 15-US spelling in MAGE-ML file. 16-Include Unapproved CV associated to the "Other" entry in MAGE-ML file, everywhere in MAGExpress. 17-Having another column in ADF; "Fail Type" which we need a OntologyEntry object for that associated with Reporter, according to the MAGE-OM. 18-In the produced mage-ml files get rid of spaces in the file name. (Replace it with UNDERLINE) 19-Fixing upload screens so that it doesn't remove the file on the server, when updating.

  posted 378 days ago

• File released: /MIAMExpress/MIAMExpress7.5/miamexpressaR7.5.tar.gz

  posted 378 days ago

• At-MIAMExpress At-MIAMExpressR1.0 file released: at-miamexpressR1.0.tar.gz

  First Release

  posted 1298 days ago

• File released: /At-MIAMExpress/At-MIAMExpressR1.0/at-miamexpressR1.0.tar.gz

  posted 1298 days ago

• MIAMExpress MIAMExpress2.0 file released: miamexpressR2.0.tar.gz

  R2.0: ===== New Features: ------------- - Experiment graph visualization and navigation. - Public standard protocols. - Experimental Factor Values. - Compressed file uploading allowed now. - Normalization and Transformation protocols. - New control vocabulary. 6 new species. 50 new journals. 2 new sexes. 1 new Sample Type. 2 new Genetic Modifications. - Removal of control vocabulary. Sample Type: biopsy, blood, faeces. - Rearranging display order of control vocabulary. Label Used. - Unselect link for protocol binding. - Change to email subject line - shorter version preferred for curators. - New CV for publication status "submitted". - Submission (array and experiment) name length changed to 255 characters. - Creating backup copies of files removed by curators. - New and updated context-sensitive help popups and main help files. - Showing the help web page after signing up. - Parsing out javascript comments for faster web page construction. - On the Create Hybridizations page, having the labeled extracts as two separate drop down boxes. - HTML anchors set up from Hybridization page back to Create Hybridizations page. - Release drop down limited to 2005/2006. - Removed javascript message submitted successfully. - Removed SampleType as mandatory. - Removed Serial Number as mandatory. - Array design submission shows local protocols only. - Form changes javascript message changed to be shorter in length. - Add and migrate new publication statuses. - Add and migrate new separation techniques. - Add and migrate new hardware and software CVs. - Add and migrate new age time point, experiment type, scanning protocol, array attachment, array platform CVs. - Species cultivar change for Oryza sativa. - New field Strain on sample page. - Accession number association to MIAMExpress experiments and arrays. - Creating new table indexes and logging off feature to improve performance. - More interface text to aid submissions. - Better and shorter javascript error messages. New Checks: ----------- 1- Checks for Affy file uploads - CHP,EXP, etc. 2- Check protocol with data file (normalization and transformation). 3- Check for at least one hybridization in an experiment submission. 4- Check for author affiliation. Needed in MAGE creation. 5- Check for forward or backward slashes in submission names. 6- Check for spaces in login name. 7- Check for duplicate submission names (array and experiment). Required for curator running of MAGE-ML scripts. 8- Check for changes in author's page before navigating away. 9- Check for hold date made more flexible for different users. 10- Check for pooling protocol if more than one sample is submitted for an extract. 11- Check for filed in sample form before navigating to extract. 12- Check to stop a form from submitting when enter is pressed except in textarea or submit button. 13- Checks for suitable names for entities - including uploaded file names. Bug Fixes: ---------- 1- Final experiment submission page had a bug when uploading a file. To do with a hidden field which was not checked for existence. 2- File upload changed to first write to disk and then to database. Avoids browser timeout errors. 3- Paste across for label extracts changed all the label extracts to associated to one extract. Fixed now. 4- Login name and password changed to length of 16. MySQL limit of 16 characters for these. 5- Curator upload and removal of files wasn't possible before since login name was curator's and not original submitters. 6- Array protocol creating in array submission page bug. Can't return to array as array wasn't submitted to database. 7- Navigating from the quality related page back to the experiment page failed. Fixed now. 8- Paste across for hybridizations changes also array id, array batch and serial number which are not expected. Fixed now. 9- Organism name change from Brachidanio rerio to Danio rerio. 10- Sorting out bug from error report for labeled extract regarding extract navigation.

  posted 1372 days ago

• File released: /MIAMExpress/MIAMExpress2.0/miamexpressR2.0.tar.gz

  posted 1372 days ago

• Tracker comment added

  sf-robot commented on the affy parsing bugs artifact

  posted by sf-robot 1406 days ago

• Tracker comment added

  sf-robot commented on the affy FGEDM artifact

  posted by sf-robot 1406 days ago

• Tracker comment added

  sf-robot commented on the Try MIAMExpress artifact

  posted by sf-robot 1406 days ago

• Tracker comment added

  sf-robot commented on the New feature:species added to array design artifact

  posted by sf-robot 1406 days ago