LSIS

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

Unstructured and/or Large Data

• Dryad Digital Repository
• figshare
• GigaDB 
• Harvard Dataverse Network
• Zenodo

Sequencing

• dbSNP
• dbVar
• Database of Genomic Variants Archive (DGVa)
• DNA DataBank of Japan (DDBJ)
• EBI Metagenomics
• EMBL Nucleotide Sequence Database (ENA)
• European Variation Archive (EVA)
• GenBank
• miRBase 
• NCBI Sequence Read Archive (SRA)
• NCBI Trace Archive
• Uniprot

Omics 

• ArrayExpress
• Database of Interacting Proteins (DIP)
• dbGAP
• The European Genome-phenome Archive (EGA)
• IntAct Molecular Interaction Database
• Gene Expression Omnibus (GEO)
• GenomeRNAi
• GPM DB
• MetaboLights
• PeptideAtlas
• Proteomics Identifications (PRIDE)
• ProteomeXchange

Structural Databases

• Biological Magnetic Resonance Data Bank (BMRB)
• Crystallography Open Database (COD)
• Coherent X-ray Imaging Data Bank (CXIDB)
• Electron Microscopy Data Bank (EMDB)
• FlowRepository
• Protein Circular Dichroism Data Bank  (PCDDB)
• Worldwide Protein Data Bank (wwPDB) 

Neuroscience 

• Functional Connectomes Project International Neuroimaging Data-Sharing Initiative (FCP/INDI)
• NeuroMorpho.org
• OpenfMRI

Model Organisms 

• Biological General Repository for Interaction Datasets (BioGRID)
• Eukaryotic Pathogen Database Resources (EuPathDB)
• FlyBase
• Mouse Genome Informatics (MGI)
• Rat Genome Database (RGD)
• SmedGD
• The Arabidopsis Information Resource (TAIR)
• VectorBase
• WormBase
• Xenbase
• Zebrafish Model Organism Database (ZFIN)

Taxonomic & Species Diversity 

• Integrated Taxonomic Information System (ITIS)
• Global Biodiversity Information Facility (GBIF) 
• NCBI Taxonomy
• The Knowledge Network for Biocomplexity

Biomedical Sciences

• Influenza Research Database
• National Addiction & HIV Data Archive Program (NAHDAP)
• National Database for Autism Research (NDAR)
• Cancer Imaging Archive
• Virtual Skeleton Database (SICAS medical image repository)
• PhysioBank

Biochemistry

• caNanoLab
• Kinetic Models of Biological Systems (KiMoSys)
• PubChem 

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

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. 

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

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

Dear visitors,

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

Please visit our services webpage.

Cheers,

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

• 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

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