1 / 10

OpenBIS Tutorial

OpenBIS Tutorial. Angela Bauch, Jan. 2008. Overview. Overview of the commands used in the command line client shown in a dependency relationship Grouped into functional sets: Registration and basic Queries of Master Data Additional Queries of Master Data Registration of Experiments

tamah
Download Presentation

OpenBIS Tutorial

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. OpenBIS Tutorial Angela Bauch, Jan. 2008

  2. Overview • Overview of the commands used in the command line client shown in a dependency relationship • Grouped into functional sets: • Registration and basic Queries of Master Data • Additional Queries of Master Data • Registration of Experiments • Basic Queries of Experiments • Basic Queries of Property Types • Registration of Property Types • Miscelleanous Commands

  3. Useful Links • Download of command line and web client application at https://wiki.systemsx.ch/display/CISDDoc/openBIS • Download of openBIS documentation & application server at https://wiki.systemsx.ch/display/bis/Download+Page • For any questions, please contact: cisd.helpdesk@systemsx.ch • When you encounter a problem using the software, you can submit an issue to our issue tracking system JIRA at https://issues.systemsx.ch:8443/secure/Dashboard.jspa

  4. Registration and basic Queries of Master Data Mandatory Input Parameters Commands Output Files Code | Registrator | Registration Date | Nucleotide Sequence ---------+-------------+---------------------+----------------------- 10468_C | Rinn, Bernd | 2007-11-08 20:03:49 | BDDHUUBUUDBUHUDDDUBDB 11015_B | Rinn, Bernd | 2007-11-08 20:03:49 | DDUUDDDHDHUHUHDBDDUBH Code | Gene Symbol Gene Id register-materials list-materials GENE MatTypeCode: GENE Code | sequ. | Inhib.code | offset Gene Id_A | Code | Registrator | Registration Date | Nucleotide Sequence ---------+-------------+---------------------+----------------------- 10468_C | Rinn, Bernd | 2007-11-08 20:03:49 | BDDHUUBUUDBUHUDDDUBDB 11015_B | Rinn, Bernd | 2007-11-08 20:03:49 | DDUUDDDHDHUHUHDBDDUBH list-materials register-materials MatTypeCode: OLIGO OLIGO Master Plate Code ------------ MP001-1 MP002-1 Code | Material.Code Well | Oligo Code register-master-plate list-master-plates filename.ext, matBatchCode Dilution Plates Bar Code | Registrator | Registration Date | Master Plate | Experiment | Project -----------+---------------+---------------------+--------------+------------+--------- DP001-1a | Rinn, Bernd | 2007-11-08 23:01:53 | MP001-1 | - | - DP002-1a | Rinn, Bernd | 2007-11-08 23:01:53 | MP002-1 | - | - Dilution Plate | Master Plate DP001-1a | MP001-1 list-dilution-plates register-dilution-plates Cell Plates Bar Code | Registrator | Registration Date | Master Plate | Dilution Plate | Experiment | Project -----------+---------------+---------------------+--------------+----------------+------------+--------- CP001-1ab | Rinn, Bernd | 2007-11-08 23:01:54 | MP001-1 | DP001-1a | EXP1 | NEMO CP002-1ac | Rinn, Bernd | 2007-11-08 23:01:54 | MP002-1 | DP002-1a | EXP1 | NEMO Cell Plate | Dilution Plate CP001-1ab | DP001-1a register-cell-plates list-cell-plates Reinfection Plates Bar Code | Registrator | Registration Date | Master Plate | Cell Plate | Experiment | Project -----------+---------------+---------------------+--------------+------------+------------+--------- RP040-1aa | Bauch, Angela | 2007-12-04 11:12:00 | MP040-1 | CP040-1aa | EXP4 | NEMO RP041-1ab | Bauch, Angela | 2007-12-04 11:12:00 | MP041-1 | CP041-1ab | EXP4 | NEMO Reinfection Plate | Cell Plate RP001-1ab | CP001-1ab list-reinfection- plates register-reinfection-plates

  5. More Queries of Master Data register-genes Master Plate Code ------------ MP001-1 MP002-1 list-master-plates register-oligos Master Plate 'MP001-1' Well | Material Batch | Oligo | Gene Id | Gene Symbol | Nucleotide Sequence ------+----------------+-------+---------+-------------+----------------------- A03 | B52 | 1_A | 1 | A1BG | DDDBBHDUUDUUDDDBDHHBH A04 | B52 | 219_A | 219 | ALDH1B1 | UDHHUHDBDDUDHDHHUHDHB register-master-plate get-plate-info Master plate code or list of codes separated by space or comma (-b) Dilution Plates Bar Code | Registrator | Registration Date | Master Plate | Experiment | Project -----------+---------------+---------------------+--------------+------------+--------- DP001-1a | Rinn, Bernd | 2007-11-08 23:01:53 | MP001-1 | - | - DP002-1a | Rinn, Bernd | 2007-11-08 23:01:53 | MP002-1 | - | - list-dilution-plates <<<Dilution Plate Information for code 'DP001-1a'>>> Registration Date: 2007-11-08 23:01:53 Registered by: brinn (Bernd Rinn) <bernd.rinn@systemsx.ch> Master Plate: MP001-1 Cell plates (generated by): CP001-1ab Master Plate 'MP001-1' Well | Material Batch | Oligo | Gene Id | Gene Symbol | Nucleotide Sequence ------+----------------+-------+---------+-------------+----------------------- A03 | B52 | 1_A | 1 | A1BG | DDDBBHDUUDUUDDDBDHHBH A04 | B52 | 219_A | 219 | ALDH1B1 | UDHHUHDBDDUDHDHHUHDHB register-dilution-plates get-plate-info Dilution plate code (-b) Cell Plates Bar Code | Registrator | Registration Date | Master Plate | Dilution Plate | Experiment | Project -----------+---------------+---------------------+--------------+----------------+------------+--------- CP001-1ab | Rinn, Bernd | 2007-11-08 23:01:54 | MP001-1 | DP001-1a | EXP1 | NEMO CP002-1ac | Rinn, Bernd | 2007-11-08 23:01:54 | MP002-1 | DP002-1a | EXP1 | NEMO register-cell-plates list-cell-plates <<<Cell Plate Information for code 'CP001-1ab'>>> Registration Date: 2007-11-08 23:01:54 Registered by: brinn (Bernd Rinn) <bernd.rinn@systemsx.ch> Dilution Plate: DP001-1a Master Plate: MP001-1 Experiment: EXP1 [project=NEMO] Consistent: yes Master Plate 'MP001-1'/Control Plate 'CL1' (marked with a star) Well | Material Batch | Oligo | Gene Id | Gene Symbol | Nucleotide Sequence ------+----------------+-------+---------+-------------+----------------------- *A01 | CL1 | SCRAM | - | - | - A03 | B52 | 1_A | 1 | A1BG | DDDBBHDUUDUUDDDBDHHBH get-plate-info Cell plate code (-b) register-reinfection -plates list-reinfection-plates

  6. Registration of Experiments register-project register-control-layout register-materials ProjCode MatTypeCode: CONTROL Code | materialCode A1 | GFP code register-experiment add-experiment-attachment ProjCode, ExpCode, filename.ext Code descr. studyObjCode studyObjTypeCodeExpTypeCode CtrlLayoutCode ProjCode CellPlates EXP1 SV40 VIRUS SIRNAHCS > CellPlates.txt Code mat.typeCode descript. FLU virus infl. A v. SV40 Code | description SIRNAHCS| small interfering RNA high content screening list-experiment-types list-study-objects experiment-type: Already stored in DB study-objects: Already stored in DB

  7. Registration of Experiments and basic Queries Code | Registrator | Registration Date EG5 | Ramin-Wright, Charles | 2007-12-04 FLT4 | Ramin-Wright, Charles | 2007-12-04 register-controls list-materials CONTROL Control Layout Code --------------- CL1 CL2 list-projects register-project register-control-layout list-control-layouts # Control Layout 'CL2' Well Code Control Code O01 GFP P01 SCRAM O02 GFP P02 SCRAM export-control-layout Control layout Code Exp. Type Study Object Descript. Registered by Reg. Date Proj. Code Exp. Properties Procedure Ctrl layout Sample: CP-0001 Measured data: Derived data: get-experiment-info ProjCode, ExpCode, GeneCode register-experiment list-experiments add-experiment-attachment get-experiment-attachment Can be restricted to study objects, projects and time intervals. Also shows study object and last data set date. ProjCode, ExpCode, filename (get from get-experiment-info output) Code descr. studyObjCode studyObjTypeCodeExpTypeCode CtrlLayoutCode ProjCode CellPlates EXP1 SV40 SIRNAHCS >CellPlates.txt

  8. Basic Queries for Property Types Property Types Code Label Data Type Material Types (* = mandatory) CELLLINE_NAME Cell line VARCHAR CELL_LINE* DESCRIPTION Description VARCHAR CELL_LINE, CONTROL, GENE, OLIGO, VIRUS GENE_SYMBOL Gene Symbol VARCHAR GENE* IS_VALID Valid? BOOLEAN - NUCLEOTIDE_SEQUENC Nucleotide Sequence VARCHAR OLIGO* OFFSET Offset INTEGER OLIGO ORG organism VARCHAR CELL_LINE* PURCHASE_DATE Purchased TIMESTAMP - REFSEQ RefSeq VARCHAR - RTPCR RT PCR REAL OLIGO VALIDATION_DATE Validated TIMESTAMP - list-property-types register-property-types as of v.17.0 timestamp & registrator Properties of materials of type OLIGO Code Label Data Type Mandatory? Description DESCRIPTION Description VARCHAR no A Description NUC_SEQ Nucl Seq VARCHAR yes A sequence of nucleotides OFFSET Offset INTEGER no Offset from the start of the sequence RTPCR RT PCR REAL no RT PCR in A459 get-material-type-info MatTypeCode: OLIGO [un]assign-material-property-types

  9. Registration of Property Types Code | description | label | dataTypeCode ORG | organism the material type was derived of | organism | VARCHAR list-property-types register-property-types filename.ext get-material-type-info [un]assign-material-property-types Mandatory: material type code, property name Optional: -m (if the flag is given, property will be mandatory) -f (a file with two columns: Code & value has to be given)

  10. Miscelleanous Commands login logout list-contacts CONTROL, GENE, OLIGO, VIRUS register-materials code MatTypeCode, filename.ext code | description CELL_LINE | Cell Line or Cell Culture. The growing of cells under controlled conditions. CONTROL | Control of a control layout GENE | Gene OLIGO | Oligo nucleotide VIRUS | Virus BACTERIUM | COMPOUND | list-material-types Code | Registrator | Registration Date | Description HAV | Bauch, Angela | 2007-12-12 11:28:03 | Hepatitis-A-Virus HBV | Bauch, Angela | 2007-12-12 11:28:03 | Hepatitis-B-Virus list-materials Material Type Code register-data-set: stored in db get-plate-locations Mandatory: Gene Symbol or Gene Id Optional: -i (if Gene Id instead of Gene Symbol) -p (Project Code) -e (Experiment Code) -o (Study Object Code) -t (Time interval) Proj.Code, Exp.Code, data-set Code, relative data-set path Example: :2007-12-10 before Dec. 10 2007 2007-08-01:2007-12-01 between Aug 1 and Dec 1 2007 now-2d last 2 days now-3d:now-5h last 3 months except last 5 hrs invalidate-plates Mandatory: plateCode Optional: -f (file with plate codes) -d (reason of invalidation) If the overriding (e.g. master) plate was invalidated then all subordinated (dilution, cell, reinfection) plates will be also invalidated. Plates hierarchy: master > dilution > cell > re-infection.

More Related