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LSIS

Recommended repositories for data publication

The PLOS journal (Public Library of Science) has published a list of recommended repositories for published data archives.

Unstructured and/or Large Data

Sequencing

Omics 

Structural Databases

Neuroscience 

Model Organisms 

Taxonomic & Species Diversity 

Biomedical Sciences

Biochemistry

See : http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories

Posted by Gaël Anex at 11:16
Swiss Open Research Data Platform

We are pleased to announce the launch of the first National Open Research Data Plaform. Have a look at www.openresearchdata.ch

Within the framework of the project Open Research Data Platform Switzerland (ORD@CH), FORS (lead institution), the Digital Humanities Lab of the University of Basel, and the ETH Scientific IT Services / SIB Swiss Institute of Bioinformatics are developing a publication platform for open research data in Switzerland. The platform will be operational as a pilot project in spring 2015. It will essentially offer a metadata catalogue of the data available at the participating institutions. 

Posted by Gaël Anex at 11:13
Our LIMS/ELN supplier awarded by the Swiss CTI commission

Great news for our LIMS/ELN supplier Genohm SA.

The company got the CTI Start-Up Label” from the Swiss Commission for Technology and Innovation (CTI). The Label is a seal of quality, of credibility and readiness for sustainable business development.

More information here

Posted by Gaël Anex at 13:55
ILab setup at SV

Dear visitors,

LSIS has started the setup and deployment of a new core facilities management software.

The software is named iLab.

Please visit the iLab website to discover all the features that we will benefit from soon.

Cheers

Posted by Gaël Anex at 13:43
LSIS website

Dear visitors,

We are pleased to announce the publication of our website lsis.epfl.ch

Please visit our services webpage.

Cheers,

 

Posted by Gaël Anex at 13:40
SLIMS update 4.6

Dear all,

Here are the novelties that come with the new version 4.6 :

- Global performance improved

- Customizable grids

- Search information in files (attachments)

- Barcodes generation with sequences

- Clear content parent action

- Copy contents/samples in ELN

- License Module

- Contents event and history (designed for clinical studies)

- Macro improved with new automated actions

https://blogs.epfl.ch/lims/documents/SLims%20Release%2046.pdf

And the bug fixed :

  1. Multiple dynamic choice that can be NA, are bugged
  2. ELN: simplified runs are not removed when trying to remove a project
  3. NA fields with groovy
  4. Drag and drop attachment in rich text do not put where the cursor stands but at the end and close the edit mode
  5. SLIMS-UPHARRIS : Impossible to delete a directory
  6. Macro : Location always show during execution in a create content step
  7. Content are not transfer to ad hoc step in 4.5
  8. Content macro step does not work if Amount not precised.
  9. Reports of type Core and table Order: cannot generate if only one content per order
  10. Slims hangs when adding a server attachment of 4Gb
  11. Impossible to create new content when cntn_id is hidden
  12. Simplified ELN: Attachment blocks: Upload of attachments via 'Choose files' button doesn't work
  13. Role with only read access can print labels
  14. Label template : field font site cannot be modified anymore
  15. Can't delete an experiment nor a block in this experiment
  16. Bug with authentification in v4.5
  17. SLIMS manual not available in 4.5
  18. Bug when create new run at SV-IN test 4.5
  19. Macro doesn't not work on 4.5
  20. Freeze when registering an order
  21. Macros: step "print label" does not happen in the right order
  22. ELN: Notes can be added under uneditable projects
  23. Add attachment from Server: user should be notified if upload fails
  24. SVIN: Unpredictible behavior of macro with print and remove steps on contents
Posted by Gaël Anex at 13:38
SLIMS 4.5 new bug fixes
  • MiSeq: automatically fetch and import sequencing files (.fastq) into SLims
  • Report templates: some bugs
  • SLims login: when accessing SLims through the page slims/Slims.html the user gets a white page and nothing happens
  • Changes to upgradeScript.sh
  • Label template : field font site cannot be modified anymore
  • Bold field are not bold when generate report since 4.5
  • Impossible to delete a dynamic choice field
  • Add attachment from Server: user should be notified if upload fails
  • ELN: Notes can be added under uneditable projects
  • SVIN: Unpredictible behavior of macro with print and remove steps on contents
  • Macros: step "print label" does not happen in the right order
  • Extra icons in SLims
  • Create new icons for EPFL-PCF
  • Reports of type Core and table Order: cannot generate if only one content per order
  • Enforce layout does not work in 4.5
  • Impossible to create new content when cntn_id is hidden
  • Content macro step does not work if Amount not precised.
  • Multiple dynamic choice that can be NA, are bugged
  • Bug when create new run at SV-IN test 4.5
  • Freeze when registering an order
  • Unactivated report templates are still usable, at least for "Core" report template.
  • Fields: value expression is not always evaluated
  • Can't delete an experiment nor a block in this experiment
  • NA fields with groovy
  • Role with only read access can print labels
  • SLIMS-UPHARRIS : Impossible to delete a directory
  • New slimsproperties files
  • ELN: simplified runs are not removed when trying to remove a project
  • Drag and drop attachment in rich text do not put where the cursor stands but at the end and close the edit mode
  • Macro : Location always show during execution in a create content step
  • Content are not transfer to ad hoc step in 4.5
  • Make possible to unshow Amount of new content in macro
  • Slims hangs when adding a server attachment of 4Gb
  • Simplified ELN: Attachment blocks: Upload of attachments via 'Choose files' button doesn't work
  • Printer configuration
  • slims-molbio: Content Management not available
  • Bug with authentification in v4.5
  • SLIMS manual not available in 4.5
  • Export "large" content list to excel doesn't work
  • Simplified protocol: add text and SOP in protocol definition
  • Fields: allow NA value
  • Multiple choice field
Posted by Gaël Anex at 13:37
SLIMS update 4.5

Dear all,

Please find below the list of bug fixes and new features that come with the new SLIMS 4.5 :

Bug fixes

  1. Macros: step "print label" does not happen in the right order
  2. ELN: Notes can be added under uneditable projects
  3. Add attachment from Server: user should be notified if upload fails
  4. Unpredictible behavior of macro with print and remove steps on contents
  5. Bug with PyRAT Pluging
  6. Drag & Drop: fails when file name contains accents
  7. Bug when drag n' drop attachment named with accent
  8. SLIMS 4.4.1 : Error when importing file with french accent in the name
  9. Error when creating a new role
  10. Forms: if first field is a dynamic choice, cursor is not positioned in it

New features

  1. Shielding: Provide role shielding on Printers
  2. Shielding: Provide role shielding on Slimsgate Flows
  3. Orders: functionalities to add/link content in OM
  4. Field of datatype multiple choice
  5. Add mechanism to see where content is unlinked
  6. ELN: Allow output linking in derivation steps
  7. Link: Remove content has been linked popup
  8. Slims upgrade scripts: automatically deploy SlimsRest
  9. Attachments: Improve UX to upload attachments
  10. Simplified ELN: enable signoff & locking
  11. Include jasperreports-htmlcomponent-5.x.y.jar
  12. Custom fields: Possibility to enter NA 
  13. Verschillende usability aanpassingen
  14. Add Groovy API to increment the sequence number for a sequence name
  15. Content: Implement 'Set original' action
  16. Content : Implement 'Merge' action
  17. Actions on big amount of records: give information to user, for example progress bar.
  18. search with wildcards in selectitems
  19. Picklists: It would be nice te be able to use multiple search words when filtering the list of choices
  20. Add multiple contents on multiple selected locations
  21. Printer configuration
  22. Labels: make location path shorter
  23. 1D Barcode code type: have the choice between "39" and "128" code types when ading the label element in the label template
  24. Label templates: Add larger font sizes - Increase the range to 1 -10
  25. Label templates: provide 'Value expression'  element - it uses a Groovy expression to fetch the value that has to be printed.
  26. Label templates: provide option to specify a Groovy expression to manipulate label element before sending it to the printer
  27. CM: By Project: Include content records that are part of a project via an order they are linked to.
  28. OM: Provide Result overview tab
  29. Simplified protocol: add text and SOP in protocol definition
  30. Export "large" content list to excel doesn't work
  31. Order module: Remove mini order grid from result tab.
  32. Report Module
  33. Fields: allow NA value
  34. Check strict fixed choices server side
  35. CM: Filter by order: Add shortcut to OM
  36. Date mask voor exacte date filters
  37. Shielding: Provide role shielding on ContentType
  38. Dynamic choice field: make choosing pick list fields more convenient
  39. Excel export/import: It should be possible to delete entire columns from an exported Excel sheet
  40. Dynamic choice custom fields: Make it possible to control the columns shown in the pick list per custom field.
  41. Multiple choice field
  42. Multiple dynamic choice field
  43. Store multiple values in a fixed choice/dynamic choice field
  44. Remove 'slimsgate flow has failed' popup from GUI
  45. Create new icons for EPFL-PCF
  46. Extra icons in SLims
  47. CM: status, it should be possible to desactivate automatic transition Available -> Labeled when printing
  48. Fixed choice drop down width should be smaller
Posted by Gaël Anex at 13:37