Related Software
Run Scanner
Run Scanner is a service that scans run directories on the file system and serves run metadata via a REST interface. MISO features integration with Run Scanner, allowing MISO to retrieve run data from Run Scanner and automatically create and update runs in MISO.
Documentation for Run Scanner can be found in its GitHub repository.
Pinery
Pinery is a REST webservice for serving LIMS data, mainly for consumption by other applications. Pinery is used as an abstraction layer to prevent other applications from depending on a specific LIMS' schema. This means that you can write applications to consume Pinery data, and then if you ever want to use a different data source, such as another LIMS, you just need a Pinery implementation for that data source and all of your existing applications will remain compatible.
Documentation for Pinery can be found in its GitHub repository. Documentation for the MISO implementation of Pinery can be found in MISO's GitHub repository.
Pinery - MISO mapping
This table describes the mapping between Pinery's Sample Provenance model and the corresponding data in MISO. Other Pinery models are not covered here.
| Pinery | Pinery example value | MISO DB | MISO UI location | |
|---|---|---|---|---|
| 1 | studyTitle | "GLCS" | Project.code, fallback Project.title | Projects > Edit Project > Code / Title |
| 2 | studyAttributes | {} | No direct MISO field | Not set in MISO UI |
| 3 | rootSampleName | "GLCS_0002" | Root ancestor Sample.alias | Samples > Edit Sample > Alias |
| 4 | parentSampleName | "GLCS_0002_Ly_R_nn_1-3_LB11: GLCS_0002_Ly_R_nn_1-3_D_S1-11: GLCS_0002_Ly_R_nn_1-3_D_263: GLCS_0002_Ly_R_nn_1-3_D_S1: GLCS_0002_Ly_R_nn_1-3: GLCS_0002" | Ancestry chain of Sample.alias / Library.alias / LibraryAliquot.name, traversed via Sample.parentId, Library.sample_sampleId, LibraryAliquot.parentAliquotId, LibraryAliquot.libraryId | Edit Sample > Alias (Parent Sample);Edit Library > Alias (Parent Sample);Edit Library Aliquot > Alias (Parent Library Aliquot) |
| 5 | sampleName | "GLCS_0002_Ly_R_nn_1-3_LB11-01" | Sample.alias / Library.alias /LibraryAliquot.alias | Samples/Libraries/Library Aliquots > Edit page > Alias |
| 6 | sampleAttributes. barcode_kit | [ "ILMN UDI Set A v3" ] | LibraryIndexFamily.name | Libraries > Edit Library > index/index family |
| 7 | sampleAttributes.geo_external_name | ["NA12878"] | Sample.externalName | Samples > Edit Sample > External Name |
| 8 | sampleAttributes. geo_group_id | [ "NA12878_6" ] | Sample.groupId / Library.groupId / LibraryAliquot.groupId | Edit Sample / Edit Library / Edit Library Aliquot > Group ID |
| 9 | sampleAttributes.geo_library_source_template_type | ["5B”] | LibraryDesignCode.code | Libraries > Edit Library > Design Code |
| 10 | sampleAttributes.geo_organism | ["Homo sapiens”] | ScientificName.alias | Samples > Edit Sample > organism/scientific name field |
| 11 | sampleAttributes.geo_prep_kit | [ "Illumina 5-Base DNA Prep" ] | KitDescriptor.name | Libraries > Edit Library > Kit / preparation kit |
| 12 | sampleAttributes.geo_purpose | ["Library”] | SamplePurpose.alias,or derived as "Stock" | Samples > Edit Sample > Purpose |
| 13 | sampleAttributes.geo_receive_date | [ "2020-08-10" ] | Transfer.transferTime date | Transfers, or received/transfer info for sample/library/aliquot |
| 14 | sampleAttributes.geo_run_id_and_position | ["9200_7"] | Run.runId + Partition.partitionNumber | Sequencer Runs > Edit Run > run ID + Run Library table partition |
| 15 | sampleAttributes.geo_str_result | ["Not Submitted"] | Sample.strStatus | Samples > Edit Sample > STR Status |
| 16 | sampleAttributes.geo_template_type | ["Illumina PE Library Seq"] | SampleClass.alias / SampleType.sampleTypeName /library type-derived sample type | Edit Sample > Sample Class / Edit Library > Library Type |
| 17 | sampleAttributes.geo_tissue_origin | ["Ly"] | TissueOrigin.alias | Samples > Edit Sample > Tissue Type |
| 18 | sampleAttributes.geo_tissue_type | ["R"] | TissueType.alias | Samples > Edit Sample > Tissue Type |
| 19 | sampleAttributes.run_purpose | ["Production"] | RunPurpose.alias | Edit Run > Partitions/Lanes or run library/aliquot table > Purpose |
| 20 | sampleAttributes.sex | ["Unknown"] | Sample.donorSex | Samples > Edit Sample > Sex |
| 21 | sampleAttributes.umis | ["False"] | Library.umis | Libraries > Edit Library > UMIs |
| 22 | sequencerRunName | "20260508_LH00000_0322_A23LNN5LT4" | Run.alias | Sequencer Runs > Edit Run > Alias |
| 23 | sequencerRunAttributes.container_model | [ "25B" ] | SequencingContainerModel.alias | Edit Container > Container Model |
| 24 | sequencerRunAttributes.instrument_name | [ "LH00000" ] | Instrument.name | Sequencer Runs > Edit Run > Instrument |
| 25 | sequencerRunAttributes.run_bases_mask | [ "y151,I10,I10,y151" ] | RunIllumina.runBasesMask | Sequencer Runs > Edit Run > Illumina/run metadata field |
| 26 | sequencerRunAttributes.run_dir | [ "/data/LH00000/20260508_LH00000_0322_A23LNN5LT4" ] | Run.filePath | Sequencer Runs > Edit Run > File Path |
| 27 | sequencerRunAttributes.sequencing_parameters | [ "2×151" ] | SequencingParameters.name | Edit Run > Partitions/Lanes > Sequencing Parameters |
| 28 | sequencerRunPlatformModel | "Illumina NovaSeq X Plus" | InstrumentModel.alias | Sequencer run > Sequencer > Instrument model "alias" |
| 29 | laneNumber | "7" | Partition.partitionNumber | Edit Run > Partitions/Lanes table > lane/partition number |
| 30 | laneAttributes.pool_name | [ "260505- April Run 12-lane 7-8" ] | Pool.alias | Pools > Edit Pool > Alias |
| 31 | laneAttributes.run_purpose | [ "Production" ] | RunPurpose.alias from lane/run partition | Edit Run > Partitions/Lanes table > Purpose |
| 32 | iusTag | "CCACCAGGCA-ATTCCATAAG" | LibraryIndex.sequence | Libraries > Edit Library > Index 1 / Index 2 |
| 33 | skip | false | Run.qcPassed / PartitionQCType.analysisSkipped / RunItemQcStatus.qcPassed / Sample.consentLevel | Edit Run > QC Status; Partitions/Lanes table > Analysis Skipped & library aliquot row QC Status; Edit Sample > Consent Level |
| 34 | sampleProvenanceId | "9200_7_LDI148800" | Run.runId + _Partition.partitionNumber + LibraryAliquot.name | Not displayed in MISO; this value is derived from the run ID, lane/partition number, and library aliquot name |
| 35 | version | "b742c895d65af242b50036de930a7499c33682fcefb2fa55917adc6792899ae6" | SHA-256 checksum of the object's fields and values, useful for detecting object modifications | Not set in UI |
| 36 | lastModified | "2026-05-19T14:16:00Z" | Sample.lastModified / Library.lastModified / LibraryAliquot.lastUpdated / Run.lastModified | Edit Sample/Library/Library Aliquot/Run metadata, system-managed |
| 37 | createdDate | "2026-05-10T00:00:00Z" | Sample.created / Library.created / LibraryAliquot.created / Run.created | Edit Sample/Library/Library Aliquot/Run metadata, system-managed |
| 38 | batchIds | [ "2026-04-30_u160_s29_k280-21017065" ] | For libraries: built from Library.creationDate, Library.creator, Library.sopId, Library.kitDescriptorId, Library.kitLot | Libraries > Edit Library > Batch > Batch ID |