Output¶
Interactive HTML report¶
An interactive and tier-structured HTML report that lists variants in in known cancer predisposition genes is provided with the following naming convention:
<sample_id>.cpsr.<genome_assembly>.html
- The sample_id is provided as input by the user, and reflects a unique identifier of the tumor-normal sample pair to be analyzed.
The report is structured in five main sections, described in more detail below:
- Settings & annotation sources
- Lists underlying tools and annotation sources (links and versions)
- Lists key configurations provided by user
- Introduction
- Describes the structure and organization of the report, as well as the predisposition genes that have been included for reporting
- Summary of findings
- Lists the top findings in Tier1/2/3
- Germline SNVs/InDels
- Comprehensive, interactive variant tables for each tier
- Tier 1
- Pathogenic variants in ClinVar
- Tier 2
- Likely pathogenic variants in ClinVar
- Tier 3
- Variants of uncertain significance - color coded by PATHRANK - a categorical variable indicating the pathogenicity of each variant based on an accumulation of ACMG evidence levels
- GWAS
- Low-risk variants found in genome-wide association studies of cancer phenotypes (NHGRI-EBI Catalog)
- References
- Supporting scientific literature (Interpretation/implementation of ACMG critera etc.)
Interactive datatables¶
The interactive datatables contain a number of hyperlinked annotations similar to those defined for the annotated VCF file, including the following:
- SYMBOL - Gene symbol (Entrez/NCBI)
- PROTEIN_CHANGE - Amino acid change (VEP)
- GENE_NAME - gene name description (Entrez/NCBI)
- PROTEIN_DOMAIN - PFAM protein domain
- PROTEIN_FEATURE - UniProt feature overlapping variant site
- CDS_CHANGE - Coding sequence change
- CONSEQUENCE - VEP consequence (primary transcript)
- HGVSc - from VEP
- HGVSp - from VEP
- ONCOGENE - Known proto-oncogene
- TUMOR_SUPPRESSOR - known tumor suppressor gene
- ONCOSCORE - Literature-derived score for oncogenic potential (gene level)
- PREDICTED_EFFECT - Effect predictions from dbNSFP
- VEP_ALL_CONSEQUENCE - All VEP consequences (multiple transcripts)
- DBSNP - dbSNP rsID
- CLINVAR - ClinVar variant origin and associated phenotypes
- GENOMIC_CHANGE - Variant ID
- GENOME_VERSION - Genome assembly
Example report¶
The HTML reports have been tested using the following browsers:
- Safari (10.0.3)
- Mozilla Firefox (52.0.2)
- Google Chrome (57.0.2987.110)
JSON¶
A JSON file that stores the HTML report content is provided. This file will easen the process of extracting particular parts of the report for further analysis. Presently, there is no detailed schema documented for the JSON structure.
Output files - germline SNVs/InDels¶
Variant call format - VCF¶
A VCF file containing annotated, germline calls (single nucleotide variants and insertion/deletions) is generated with the following naming convention:
<sample_id>.cpsr.<genome_assembly>.vcf.gz (.tbi)
Here, the sample_id is provided as input by the user, and reflects a unique identifier of the tumor-normal sample pair to be analyzed. Following common standards, the annotated VCF file is compressed with bgzip and indexed with tabix. Below follows a description of all annotations/tags present in the VCF INFO column after processing with the CPSR annotation pipeline:
VEP consequence annotations¶
- CSQ - Complete consequence annotations from VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON| INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids| Codons|Existing_variation|ALLELE_NUM|DISTANCE|STRAND|FLAGS|PICK|VARIANT_CLASS| SYMBOL_SOURCE|HGNC_ID|CANONICAL|APPRIS|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC| RefSeq|DOMAINS|HGVS_OFFSET|AF|AFR_AF|AMR_AF|EAS_AF|EUR_AF|SAS_AF|gnomAD_AF| gnomAD_AFR_AF|gnomAD_AMR_AF|gnomAD_ASJ_AF|gnomAD_EAS_AF|gnomAD_FIN_AF| gnomAD_NFE_AF|gnomAD_OTH_AF|gnomAD_SAS_AF|CLIN_SIG|SOMATIC|PHENO| MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE
- Consequence - Impact modifier for the consequence type (picked by VEP’s –flag_pick_allele option)
- Gene - Ensembl stable ID of affected gene (picked by VEP’s –flag_pick_allele option)
- Feature_type - Type of feature. Currently one of Transcript, RegulatoryFeature, MotifFeature (picked by VEP’s –flag_pick_allele option)
- Feature - Ensembl stable ID of feature (picked by VEP’s –flag_pick_allele option)
- cDNA_position - Relative position of base pair in cDNA sequence (picked by VEP’s –flag_pick_allele option)
- CDS_position - Relative position of base pair in coding sequence (picked by VEP’s –flag_pick_allele option)
- CDS_CHANGE - Coding, transcript-specific sequence annotation (picked by VEP’s –flag_pick_allele option)
- AMINO_ACID_START - Protein position indicating absolute start of amino acid altered (fetched from Protein_position)
- AMINO_ACID_END - Protein position indicating absolute end of amino acid altered (fetched from Protein_position)
- Protein_position - Relative position of amino acid in protein (picked by VEP’s –flag_pick_allele option)
- Amino_acids - Only given if the variant affects the protein-coding sequence (picked by VEP’s –flag_pick_allele option)
- Codons - The alternative codons with the variant base in upper case (picked by VEP’s –flag_pick_allele option)
- IMPACT - Impact modifier for the consequence type (picked by VEP’s –flag_pick_allele option)
- VARIANT_CLASS - Sequence Ontology variant class (picked by VEP’s –flag_pick_allele option)
- SYMBOL - Gene symbol (picked by VEP’s –flag_pick_allele option)
- SYMBOL_SOURCE - The source of the gene symbol (picked by VEP’s –flag_pick_allele option)
- STRAND - The DNA strand (1 or -1) on which the transcript/feature lies (picked by VEP’s –flag_pick_allele option)
- ENSP - The Ensembl protein identifier of the affected transcript (picked by VEP’s –flag_pick_allele option)
- FLAGS - Transcript quality flags: cds_start_NF: CDS 5’, incomplete cds_end_NF: CDS 3’ incomplete (picked by VEP’s –flag_pick_allele option)
- SWISSPROT - Best match UniProtKB/Swiss-Prot accession of protein product (picked by VEP’s –flag_pick_allele option)
- TREMBL - Best match UniProtKB/TrEMBL accession of protein product (picked by VEP’s –flag_pick_allele option)
- UNIPARC - Best match UniParc accession of protein product (picked by VEP’s –flag_pick_allele option)
- HGVSc - The HGVS coding sequence name (picked by VEP’s –flag_pick_allele option)
- HGVSp - The HGVS protein sequence name (picked by VEP’s –flag_pick_allele option)
- HGVSp_short - The HGVS protein sequence name, short version (picked by VEP’s –flag_pick_allele option)
- HGVS_OFFSET - Indicates by how many bases the HGVS notations for this variant have been shifted (picked by VEP’s –flag_pick_allele option)
- MOTIF_NAME - The source and identifier of a transcription factor binding profile aligned at this position (picked by VEP’s –flag_pick_allele option)
- MOTIF_POS - The relative position of the variation in the aligned TFBP (picked by VEP’s –flag_pick_allele option)
- HIGH_INF_POS - A flag indicating if the variant falls in a high information position of a transcription factor binding profile (TFBP) (picked by VEP’s –flag_pick_allele option)
- MOTIF_SCORE_CHANGE - The difference in motif score of the reference and variant sequences for the TFBP (picked by VEP’s –flag_pick_allele option)
- CELL_TYPE - List of cell types and classifications for regulatory feature (picked by VEP’s –flag_pick_allele option)
- CANONICAL - A flag indicating if the transcript is denoted as the canonical transcript for this gene (picked by VEP’s –flag_pick_allele option)
- CCDS - The CCDS identifier for this transcript, where applicable (picked by VEP’s –flag_pick_allele option)
- INTRON - The intron number (out of total number) (picked by VEP’s –flag_pick_allele option)
- EXON - The exon number (out of total number) (picked by VEP’s –flag_pick_allele option)
- DOMAINS - The source and identifier of any overlapping protein domains (picked by VEP’s –flag_pick_allele option)
- DISTANCE - Shortest distance from variant to transcript (picked by VEP’s –flag_pick_allele option)
- BIOTYPE - Biotype of transcript or regulatory feature (picked by VEP’s –flag_pick_allele option)
- TSL - Transcript support level (picked by VEP’s –flag_pick_allele option)>
- PUBMED - PubMed ID(s) of publications that cite existing variant - VEP
- PHENO - Indicates if existing variant is associated with a phenotype, disease or trait - VEP
- GENE_PHENO - Indicates if overlapped gene is associated with a phenotype, disease or trait - VEP
- ALLELE_NUM - Allele number from input; 0 is reference, 1 is first alternate etc - VEP
- REFSEQ_MATCH - The RefSeq transcript match status; contains a number of flags indicating whether this RefSeq transcript matches the underlying reference sequence and/or an Ensembl transcript (picked by VEP’s –flag_pick_allele option)
- PICK - Indicates if this block of consequence data was picked by VEP’s –flag_pick_allele option
- VEP_ALL_CONSEQUENCE - All transcript consequences (Consequence:SYMBOL:Feature_type:Feature:BIOTYPE) - VEP
Gene information¶
- ENTREZ_ID - Entrez gene identifier
- APPRIS - Principal isoform flags according to the APPRIS principal isoform database
- UNIPROT_ID - UniProt identifier
- UNIPROT_ACC - UniProt accession(s)
- ENSEMBL_GENE_ID - Ensembl gene identifier for VEP’s picked transcript (ENSGXXXXXXX)
- ENSEMBL_TRANSCRIPT_ID - Ensembl transcript identifier for VEP’s picked transcript (ENSTXXXXXX)
- REFSEQ_MRNA - Corresponding RefSeq transcript(s) identifier for VEP’s picked transcript (NM_XXXXX)
- CORUM_ID - Associated protein complexes (identifiers) from CORUM
- DISGENET_CUI - Tumor types associated with gene, as found in DisGeNET. Tumor types are listed as unique MedGen concept IDs (CUIs)
- TUMOR_SUPPRESSOR - Gene is predicted as tumor suppressor candidate according to (CancerMine)
- ONCOGENE - Gene is predicted as an oncogene according to (CancerMine)
- ONCOSCORE - Literature-derived score for cancer gene relevance Bioconductor/OncoScore, range from 0 (low oncogenic potential) to 1 (high oncogenic potential)
- CANCER_SUSCEPTIBILITY_CUI - MedGen concept unique identifier (CUI) for cancer phenotype
- CANCER_SYNDROME_CUI - MedGen concept unique identifier (CUI) for cancer syndrome
- CANCER_PREDISPOSITION_SOURCE - Data source for susceptibility gene (NCGC, CGC, TCGA_PANCAN)
- CANCER_PREDISPOSITION_MOI - Mechanism of inheritance for susceptibility gene (AR/AD)
- CANCER_PREDISPOSITION_MOD - Mechanism of disease for susceptibility gene (Lof/GoF)
Variant effect and protein-coding information¶
- MUTATION_HOTSPOT - mutation hotspot codon in cancerhotspots.org. Format: gene_symbol | codon | q-value
- MUTATION_HOTSPOT_TRANSCRIPT - hotspot-associated transcripts (Ensembl transcript ID)
- MUTATION_HOTSPOT_CANCERTYPE - hotspot-associated cancer types (from cancerhotspots.org)
- UNIPROT_FEATURE - Overlapping protein annotations from UniProt KB
- PFAM_DOMAIN - Pfam domain identifier (from VEP)
- EFFECT_PREDICTIONS - All predictions of effect of variant on protein
function and pre-mRNA splicing from database of non-synonymous
functional predictions - dbNSFP
v3.5. Predicted
effects are provided by different sources/algorithms (separated by
‘&’):
- SIFT (Jan 2015)
- LRT (2009)
- MutationTaster (data release Nov 2015)
- MutationAssessor (release 3)
- FATHMM (v2.3)
- PROVEAN (v1.1 Jan 2015)
- FATHMM_MKL
- DBNSFP_CONSENSUS_SVM (Ensembl/consensus prediction, based on support vector machines)
- DBNSFP_CONSENSUS_LR (Ensembl/consensus prediction, logistic regression based)
- SPLICE_SITE_EFFECT_ADA (Ensembl/consensus prediction of splice-altering SNVs, based on adaptive boosting)
- SPLICE_SITE_EFFECT_RF (Ensembl/consensus prediction of splice-altering SNVs, based on random forest)
- M-CAP
- MutPred
- GERP
- SIFT_DBNSFP - predicted effect from SIFT (dbNSFP)
- PROVEAN_DBNSFP - predicted effect from PROVEAN (dbNSFP)
- MUTATIONTASTER_DBNSFP - predicted effect from MUTATIONTASTER (dbNSFP)
- MUTATIONASSESSOR_DBNSFP - predicted effect from MUTATIONASSESSOR (dbNSFP)
- M_CAP_DBNSFP - predicted effect from M-CAP (dbNSFP)
- MUTPRED_DBNSFP - score from MUTPRED (dbNSFP)
- FATHMM_DBNSFP - predicted effect from FATHMM (dbNSFP)
- FATHMM_MKL_DBNSFP - predicted effect from FATHMM-mkl (dbNSFP)
- META_LR_DBNSFP - predicted effect from ensemble prediction (logistic regression - dbNSFP)
- SPLICE_SITE_RF_DBNSFP - predicted effect of splice site disruption, using random forest (dbscSNV)
- SPLICE_SITE_ADA_DBNSFP - predicted effect of splice site disruption, using boosting (dbscSNV)
Variant frequencies/annotations in germline databases¶
- AFR_AF_GNOMAD - African/American germline allele frequency (Genome Aggregation Database release 2)
- AMR_AF_GNOMAD - American germline allele frequency (Genome Aggregation Database release 2)
- GLOBAL_AF_GNOMAD - Adjusted global germline allele frequency (Genome Aggregation Database release 2)
- SAS_AF_GNOMAD - South Asian germline allele frequency (Genome Aggregation Database release 2)
- EAS_AF_GNOMAD - East Asian germline allele frequency (Genome Aggregation Database release 21)
- FIN_AF_GNOMAD - Finnish germline allele frequency (Genome Aggregation Database release 2)
- NFE_AF_GNOMAD - Non-Finnish European germline allele frequency (Genome Aggregation Database release 2)
- OTH_AF_GNOMAD - Other germline allele frequency (Genome Aggregation Database release 2)
- ASJ_AF_GNOMAD - Ashkenazi Jewish allele frequency (Genome Aggregation Database release 2)
- AFR_AF_1KG - 1000G Project - phase 3 germline allele frequency for samples from AFR (African)
- AMR_AF_1KG - 1000G Project - phase 3 germline allele frequency for samples from AMR (Ad Mixed American)
- EAS_AF_1KG - 1000G Project - phase 3 germline allele frequency for samples from EAS (East Asian)
- EUR_AF_1KG - 1000G Project - phase 3 germline allele frequency for samples from EUR (European)
- SAS_AF_1KG - 1000G Project - phase 3 germline allele frequency for samples from SAS (South Asian)
- GLOBAL_AF_1KG - 1000G Project - phase 3 germline allele frequency for all 1000G project samples (global)
- DBSNPRSID - dbSNP reference ID, as provided by VEP
Clinical associations¶
- CLINVAR_MSID - ClinVar Measure Set/Variant ID
- CLINVAR_ALLELE_ID - ClinVar allele ID
- CLINVAR_PMID - Associated Pubmed IDs for variant in ClinVar - germline state-of-origin
- CLINVAR_HGVSP - Protein variant expression using HGVS nomenclature
- CLINVAR_PMID_SOMATIC - Associated Pubmed IDs for variant in ClinVar - somatic state-of-origin
- CLINVAR_CLNSIG - Clinical significance for variant in ClinVar - germline state-of-origin
- CLINVAR_CLNSIG_SOMATIC - Clinical significance for variant in ClinVar - somatic state-of-origin
- CLINVAR_MEDGEN_CUI - Associated MedGen concept identifiers (CUIs) - germline state-of-origin
- CLINVAR_MEDGEN_CUI_SOMATIC - Associated MedGen concept identifiers (CUIs) - somatic state-of-origin
- CLINVAR_VARIANT_ORIGIN - Origin of variant (somatic, germline, de novo etc.) for variant in ClinVar
- GWAS_HIT - variant associated with cancer phenotype from genome-wide association study (NHGRI-EBI GWAS catalog)
Tab-separated values (TSV)¶
Annotated List of all SNVs/InDels¶
We provide a tab-separated values file with most important variant/gene annotations. The file has the following naming convention:
<sample_id>.cpsr.<genome_assembly>.snvs_indels.tiers.tsv
The SNVs/InDels are organized into different tiers (as defined above for the HTML report)
The following variables are included in the tiered TSV file:
1. GENOMIC_CHANGE - Identifier for variant at the genome (VCF) level, e.g. 1:g.152382569A>G
Format: (<chrom>:g.<position><ref_allele>><alt_allele>)
2. VAR_ID - Variant identifier
3. GENOTYPE - Variant genotype (heterozygous/homozygous)
4. GENOME_VERSION - Assembly version, e.g. GRCh37
5. VCF_SAMPLE_ID - Sample identifier
6. VARIANT_CLASS - Variant type, e.g. SNV/insertion/deletion
7. CODING_STATUS - coding/noncoding (wrt. protein alteration and canonical splice site disruption)
8. SYMBOL - Gene symbol
9. GENE_NAME - Gene description
10. CCDS - CCDS identifier
11. ENTREZ_ID - Entrez gene identifier
12. UNIPROT_ID - UniProt protein identifier
13. ENSEMBL_GENE_ID - Ensembl gene identifier
14. ENSEMBL_TRANSCRIPT_ID - Ensembl transcript identifier
15. REFSEQ_MRNA - RefSeq mRNA identifier
16. ONCOSCORE - Literature-derived score for cancer gene relevance
17. ONCOGENE - Gene is predicted as an oncogene according to literature mining (CancerMine)
18. TUMOR_SUPPRESSOR - Gene is predicted as tumor suppressor according to literature mining (CancerMine)
19. MOD - Mechanism of disease for cancer predisposition gene (Lof/GoF/NA)
20. PATH_TRUNCATION_RATE - Rate of pathogenic truncations in predisposition gene
21. BENIGN_MISSENSE_RATE - Rate of benign missense mutations in predisposition gene
22. CONSEQUENCE - Variant consequence
23. PROTEIN_CHANGE - Protein change - one letter abbreviation (HGVSp)
24. PROTEIN_DOMAIN - Protein domain description from PFAM
25. HGVSp - The HGVS protein sequence name
26. HGVSc - The HGVS coding sequence name
27. CDS_CHANGE - Coding, transcript-specific sequence annotation
28. MUTATION_HOTSPOT - Cancer mutation hotspot (cancerhotspots.org)
29. RMSK_HIT - RepeatMasker hit
30. PROTEIN_FEATURE - Protein feature (active sites etc.) from UniProt KnowledgeBase
31. EFFECT_PREDICTIONS - Functional effect predictions from multiple algorithms (dbNSFP)
32. LOSS_OF_FUNCTION - Loss-of-function variant, as predicted from VEP's LofTee plugin
33. DBSNP - dbSNP identifier
34. CLINVAR_CLINICAL_SIGNIFICANCE - clinical significance of ClinVar variant
35. CLINVAR_MSID - measureset identifier of ClinVar variant
36. CLINVAR_VARIANT_ORIGIN - variant origin (somatic/germline) of ClinVar variant
37. CLINVAR_CONFLICTED - indicator of conflicting interpretations
38. CLINVAR_PHENOTYPE - associated phenotype(s) for ClinVar variant
39. VEP_ALL_CONSEQUENCE - all consequences from VEP
40. PATHSCORE - Composite variant pathogenicity score
41. PATHRANK - Categorical ranking of pathogenicity (HIGH,MODERATE,LOW,BENIGN)
42. PATHDOC - Documentation for PATHSCORE/PATHRANK
43. PVS1 - ACMG criteria: Null variant (nonsense, frameshift, canonical ±1 or 2 splice sites, initiation codon, single or multiexon deletion) - in a gene where LoF is a known mechanism of disease (Dom MoI)
44. PSC1 - ACMG criteria: Null variant (nonsense, frameshift, canonical ±1 or 2 splice sites, initiation codon, single or multiexon deletion) - in a gene where LoF is a known mechanism of disease (Rec MoI)
45. PS1 - ACMG criteria: Same amino acid change as a previously established pathogenic variant regardless of nucleotide change
46. PMC1 - ACMG criteria: Null variant in a gene where LoF is not a known mechanism of disease
47. PM1 - ACMG criteria: Variant located in mutation hotspot (cancerhotspots.org)
48. PM2 - ACMG criteria: Absence or extremely low frequency (MAF < 0.0005) in 1000 Genomes Project, or gnomAD
49. PM4 - ACMG criteria: Protein length changes due to inframe indels or nonstop variant in non-repetitive regions of genes that harbor variants with a Dom MoI.
50. PM5 - ACMG criteria: Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before
51. PP2 - ACMG criteria: Missense variant in a gene that has a relatively low rate of benign missense variation (<20%) and where missense variants are a common mechanism of disease (>50% of pathogenic variants)
52. PPC1 - ACMG criteria: Protein length changes due to inframe indels or nonstop variant in non-repetitive regions of genes that harbor variants with a Rec MoI.
53. PP3 - ACMG criteria: Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc. - from dbNSFP)
54. BP4 - ACMG criteria: Multiple lines of computational evidence support a benign effect on the gene or gene product (conservation, evolutionary, splicing impact, etc. - from dbNSFP).
55. BMC1 - ACMG criteria: Peptide change is at the same location of a known benign change
56. BSC1 - ACMG criteria: Peptide change is known to be benign
57. BA1 - ACMG criteria: Common population frequency (MAF > 0.05) in 1000 Genomes Project, or gnomAD
58. BP1 - ACMG criteria: Missense variant in a gene for which primarily truncating variants (>90%) are known to cause disease
59. N_INSILICO_CALLED - Number of algorithms with effect prediction (damaging/tolerated) from dbNSFP
60. N_INSILICO_DAMAGING - Number of algorithms with damaging prediction from dbNSFP
61. N_INSILICO_TOLERATED - Number of algorithms with tolerated prediction from dbNSFP
62. N_INSILICO_SPLICING_NEUTRAL - Number of algorithms with splicing neutral prediction from dbscSNV
63. N_INSILICO_SPLICING_AFFECTED - Number of algorithms with splicing affected prediction from dbscSNV
64. GLOBAL_AF_GNOMAD - Global MAF in gnomAD
65. <CUSTOM_POPULATION_GNOMAD> - Population specific MAF in gnomAD (population configured by user)
66. GLOBAL_AF_1KG - Global MAF in 1000 Genomes Project
67. <CUSTOM_POPULAION_1KG> - Population-specific MAF in 1000 Genomes Project (population configured by user)
68. TIER - CPSR tier level
69. TIER_DESCRIPTION - Description of CPSR tier
NOTE: The user has the possibility to append the TSV file with data from other tags in the input VCF of interest (i.e. using the custom_tags option in the TOML configuration file)


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Bill Russell finally accepts Basketball Hall of Fame ring
SPRINGFIELD, MASSACHUSETTS – Bill Russell finally accepted his Basketball Hall of Fame ring.
The 11-time NBA champion, five-time MVP, Olympic gold medalist and two-time NCAA champ said on Twitter on Friday that he was presented with his Hall of Fame ring in a private ceremony.
The 85-year-old Boston Celtics great didn’t attend the induction ceremony in 1975. He said he didn’t deserve to be the first black player inducted, tweeting: “I felt others before me should have that honor.”
His tweet mentions Chuck Cooper, who in 1950 was the first African-American player drafted by the NBA and who was posthumously inducted this year.
Russell said the ceremony was attended by his wife, along with close friends and Hall of Famers Bill Walton, Ann Meyers and Alonzo Mourning.
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| void | set_id (const size_t my_id_in) |
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| size_t | get_id () const |
| | Getter for the Zone ID in its Mesh (Zone::my_id) More...
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| FacePtr | get_face (const short int i) const |
| | Getter for the i-th Face within *this Zone (Zone::face) More...
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| double | get_ne () const |
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| | Setter for the electron temperature (Zone::te) More...
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| double | get_te () const |
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| std::string | mat_at (const unsigned short int i) const |
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| const std::vector< std::string > & | get_mat () const |
| | Getter for material IDs (Zone::mat) More...
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| double | fp_at (const unsigned short int i) const |
| | Getter for the fraction of a specific material (Zone::fp) More...
|
| |
| const std::vector< double > & | get_fp () const |
| | Getter for material fractions (Zone::fp) More...
|
| |
| size_t | size () const |
| | Getter for the number of Face objects for *this Zone. More...
|
| |
| Vector3d | zone_point (const Grid &g, const Vector3d &p) const |
| | Calculates a reference point within *this Zone. More...
|
| |
| RetIntercept | hit (const Grid &g, const Vector3d &p, const Vector3d &u, const FaceID &fid) const |
| | Calculates the hit-point where a Ray enters *this Zone. More...
|
| |
| std::string | to_string () const |
| | String representation of a Zone object. More...
|
| |
| void | load_geo (std::ifstream &geometry) |
| | Loads geometry (Face shapes and sizes) info from input file;
assumes utils::find_word (geometry, "Zone") has already been called. More...
|
| |
| void | load_mat (std::ifstream &material) |
| | Loads material info (temperatures, densities) from input file;
assumes Zone::load_geo (geometry) has already been called,
assumes utils::find_word (material, "Zone") has already been called. More...
|
| |
| void | load_spectra (const Database &d, const Table &tbl, size_t &ite, size_t &itr, size_t &ine, const std::string &symmetry, const size_t ix, const bool analysis, const size_t jmin, const size_t jmax, ArrDbl &em, ArrDbl &ab, ArrDbl &sc) |
| | Builds mixed monochromatic optical data for *this Zone;
if symmetry != "none", also either stores newly computed data
(Zone::emis, Zone::absp, Zone::scat) or retrieves them.
Assumes Zone::load_mat (material) has already been called. More...
|
| |
| std::string | mat_to_string_full () const |
| | Full string representation of materials in *this Zone. More...
|
| |
| std::string | mat_to_string_plot () const |
| | Abbreviated string representation of materials in *this Zone. More...
|
| |
Spatial zone, defined by a list bounding Face objects.
Definition at line 31 of file Zone.h.


MY MISSION: to help free the human spirit and propel consciousness forward by providing grounded and balanced information that elevates awareness and understanding.
This website reflects my perpetual desire to connect with like-minded people and those who are inspired enough by my efforts to consider combining our skills and knowledge to co-create a better world and brighter future. I hope this website inspires others to express their own interests and passions and to elevate their personal mission to a higher level.
I'm free open source user FOSS
I'm also a volunteer member of a FREE SOFTWARE FOUNDATION OF TAMILNADU FSFTN and also a volunteer member of SJIT(GNU-LINUX-USERS-GROUP)
I am a volunteer and member of SJIT GNU linux users group
I love to work on Ruby on rails (framework) and creating a projects on it
Learning to program in Ruby is much easier than in other languages because the language is super flexible
Rails is so fun for beginners is because it’s really really robust and it does SO MUCH of the hard work for you.
MY Projects are displayed in GITHUB
You can visit my upcoming and present projects on my github page.
Visit Github PageYou can visit my personal blog
You can visit our collabarative Blog
Visit Common BlogSpend some time on Data security and computer stuffs
Dont_Be_InfectedLets play our vintage games :P
Bounce


Offers created by the stores
Images of Offers created by the stores
FOOD
SHOPPING
SALOON&SPA
ENTERTAINMENT


{% extends "ksp_login/base.html" %} {% load i18n %} {% block ksp_login_title %}{% trans "Registration" %}{% endblock ksp_login_title %} {% block page_header %}
{% trans "Welcome, new user. You only need to give us a few details in order to finish the registration process." %}
{% include "ksp_login/parts/multiple_forms.html" %} {% endblock ksp_login_content %}


{% extends "base.html" %}
{% load breadcrumbs %}
{% block title %}Create Role in Project {{ project.name }}{% endblock %}
{% block head %}
{% endblock %}
{% block content %}
Create Role in Project {{ project.name }}
Here you can create new roles in the project. Select the permissions
you would like users with this role to have, select a unique name
for the role in the project, add a description, and save.


A three-day virtual experience that will inspire and engage our generation to vote!
Oct 30 - Nov 1
#BECOMINGAMERICAFEST
The people are voting.
The election is now.
Festival Schedule
ALL TIMES EASTERN
Day 1: October 30
Kalen Allen
Ashley Everett
Blake Gray
Charles Brockman III
Isabella Gomez
Avani Gregg
Amelie Zilber
Day 1: October 30
Kalen Allen
Charles Brockman III
Ashley Everett
Blake Gray
Isabella Gomez
Avani Gregg
Amelie Zilber
Day 2: October 31
Jimmie Allen
Huw Collins
Meg Donnelly
Ian Harding
Sammy Jaye
Manny Mua
PatrickStarr
Karan Brar
Shea Diamond
Aliya Grace
Karlton Humes
Max Joseph
Sarah Schauer
Naomi Wadler
Jessie Woo
Day 2: October 31
Jimmie Allen
Karan Brar
Huw Collins
Shea Diamond
Meg Donnelly
Aliya Grace
Ian Harding
Karlton Humes
Sammy Jaye
Max Joseph
Manny Mua
Sarah Schauer
PatrickStarr
Naomi Wadler
Jessie Woo
Day 3: November 1
Charlie Carver
Christopher Davis
Skai Jackson
Serena Kerrigan
Gracie Pekrul
TwinsTheNewTrend
Noah Centineo
Theo Germaine
JVCKJ
Jillian Mercado
Yara Shahidi
Gabriel Zamora
Day 3: November 1
Charlie Carver
Noah Centineo
Christopher Davis
Theo Germaine
Skai Jackson
JVCKJ
Serena Kerrigan
Jillian Mercado
Gracie Pekrul
Yara Shahidi
TwinsTheNewTrend
Gabriel Zamora


Paranoia is a funny thing. At the time it seems seriously scary. Then later on, you remember what you were paranoid about and laugh about it.
I've seldom been seriously paranoid. Usually it's those times when I get stoned thinking I have nothing to do, then I realise that I have to go to some social thing and interract. I don't think I've actually experienced proper paranoia for about a year or two... But I digress.
My most paranoid moment was a few years ago. We used to have regular parties at my friend Keef's place. Myself, A, Wab, Phlo... occasionally Rolo would be there too.  As this sort of thing happened quite often, we were all fairly hardened smokers by this point. Amyway, at this particular point late in the evening, I was feeling seriously stoned. We'd had a serious amount each to smoke -- from a couple of blocks of resin that both A and myself had, and a bit of Keef's homegrown.
It was late in the evening. Probably about 10, and we'd all arrived around 7. A was debating something or other with Keef. The girls sat mostly listening, party talking to each other and giggling. Rolo was rolling another spliff. I was sitting in an armchair, facing the others. In the candlelight, the room looked dim. I suddenly had the unshakeable feeling I was being watched. Out of the corner of my eye, I could see the doorway to the lounge where I was certain a tall black cat sat watching my every move.
I felt rooted to the spot. I was certain this cat was evil. In fact, I began to grow more and more convinced that it was Satan himself. I started to be scared about having to eventually leave, because the cat would get me.
I was lost in all these turbulent thoughts behind my glazed eyes for what seemed like an hour.
'Wake up!' I was shaken out of it suddenly. Phlo was holding a spliff out to me, and I realised I'd been staring blankly for what turned out to be only a few minutes.
I took the spliff from her, took a drag and then laughed at my paranoia attack.
Paranoia is a funny thing.
Experience Reports are the writings and opinions of the individual authors who submit them.
Some of the activities described are dangerous and/or illegal and none are recommended by Erowid.


Copy
(Edit ->Copy or Ctrl+C)Click on the Copy icon. Move the cursor to the design window, and delimit the active area with the mouse. Consequently, all the graphics included in this area are copied. The external shape of the copied elements appears. Fix those copied elements at the desired location by a click on the mouse.
Click on Undo to cancel the copy command.
[Back]


XF Generator allows you to update sources and dependencies:
yo xf:update [all]
— update less and js files of XFramework, check latest versions of jQuery, Backbone, Underscoreyo xf:update scripts
— update js files (inluding thirdparty libraries) of XFramework, check latest versions of jQuery, Backbone, Underscoreyo xf:update styles
— update less files of XFramework


splithalf_documentation
Sam Parsons
2018-11-13
1 Start-up notes
1.1 Instalation
The splithalf package can be installed from CRAN or Github:
install.packages("splithalf")
# or the development version
# devtools::install_github("sdparsons/splithalf")
also note that the package requires the following; tidyr, dplyr, Rcpp, robustbase. You can load them with the following
library("tidyr")
library("dplyr")
library("Rcpp")
library("robustbase")
1.2 Version note
The current version of splithalf is 0.5.1 [unofficial version name: Fight Milk]
A huge part of developing this latest version has been condensing the many splithalf functions into a single one. In addition to this, I have adapted the underlying code using the amazing Rcpp package (Eddelbuettel et al. 2018), enabling me to input some C++ code. While my C++ code is rudimentary, the splithalf function now runs around 20x faster than before.
1.3 Citing the package
Citing packages is one way for developers to gain some recognition for the time spent maintaining the work. I would like to keep track of how the package is used so that I can solicit feedback and improve the package more generally. This would also help me track the uptake of reporting measurement reliability over time.
Please use the following reference: Parsons, S. (2017). splithalf: robust estimates of split half reliability (Version 2). figshare. https://doi.org/10.6084/m9.figshare.5559175.v2
If (eventually) this documentation turns into a publication, this reference will change.
1.4 User feedback
Developing the splithalf package is a labour of love (and, occasionally, burning hatred). If you have any suggestions for improvement, additional functionality, or anything else, please contact me or raise an issue on github. Likewise, if you are having trouble using the package (e.g. scream fits at your computer screen – we’ve all been there) do contact me and I will do my best to help as quickly as possible. These kind of help requests are super welcome. In fact, the package has seen several increases in performance and usability due to people asking for help.
1.5 A note on terminology used in this document
It is important that we have a similar understanding of the terminology I use in the package and documentation. Each is also discussed in reference to the functions later in the documentation.
- Trial – whatever happens in this task, e.g. a stimuli is presented. Importantly, participants give one response per trial
- Trial type – often trials can be split into different trial types (e.g. to compare congruent and incongruent trials)
- Condition - this might be different blocks of trials, or something to be assessed separately within the functions. e.g. a task might have a block of ‘positive’ trials and a block of ‘negative’ trials.
- Datatype - I use this to refer to the outcome of interest. specifically whether one is interested in average response times or accuracy rates
- Score - I use score to indicate how the final outcome is measured; e.g. the average RT, or the difference between two average RTs, or even the difference between two differences between two RTs (yes, the final one is confusing)
References
Eddelbuettel, Dirk, Romain Francois, JJ Allaire, Kevin Ushey, Qiang Kou, Nathan Russell, Douglas Bates, and John Chambers. 2018. Rcpp: Seamless R and C++ Integration. https://CRAN.R-project.org/package=Rcpp.


| Path: | README |
| Last Update: | Mon May 17 15:10:17 +0100 2010 |
A plugin that supports linking of Models within a RoR application to a Concept and Ontology within the BioPortal
Also includes a Mixin and a Helper to facilitate making use of the Rest API without linking to a Model.
More information about BioPortal, and its Rest API, may be found at:
bioportal.bioontology.org/ (main Portal)
www.bioontology.org/wiki/index.php/BioPortal_REST_services (Rest services).
Install the plugin from sysmo-db.googlecode.com/hg/vendor/plugins/bioportal
Since the rails plugin scripts don‘t work happily with Mercurial, until we extract this plugin the simplest way of adding the plugin is as follows:
cd vendor/plugins hg clone https://sysmo-db.googlecode.com/hg/vendor/plugins/bioportal bioportal rm -rf bioportal/.hg/ cd -
Generate the database migration by running
./script/generate bioportal_migration
This generates a table that maps to the BioportalConcept entity, though you don‘t need to know about this in your application.
To link to a model in your RoR application, add the following line to your Model class
class MyThing < ActiveRecord::Base linked_to_bioportal<EMAIL_ADDRESS>... end
adding :email is optional, but recommended as you will be notified of changes to the REST API.
You can also use :base_url to indicate a different deployment of BioPortal than the default, which is rest.bioontology.org/bioportal/
This then provides your model with the attributes:
ontology_id ontology_version_id concept_uri
which once set allows you to call the method concept to retreive information about that concept, such as its synonyms, parents and children.
and you can also call the method ‘ontology’ to reteive information about the ontology.
More information about this can be found in the API documentation.
by adding the include
include BioPortal::RestAPI
you can find out more by reading BioPortal::RestAPI
Some view helpers are automatically injected into your application and you don‘t need to do anything to use them.
You can find out more about these by reading about BioPortalHelper


title = "resource listing" url = "/resources/listing" layout = "restricted" is_hidden = 0 ==
Some quick example text to build on the card title and make up the bulk of the card's content.
1234 Main St
Wichita, KS 67202
(316) 265-5211
$250/mo


Marco's Backyard Swimming operates "www.marcosbackyardswimming.ca". This page informs you of our policies regarding the collection, use and disclosure of Personal Information we recieve from users of our site.
We use your Personal Information none other then when you (the user) sends us an email using our form. No information is stored beyond the contents in the email and the informations disclosed during the modes of connecting with you afterwards.
While using our site, we may ask you to provide us with certain personally identifiable information that can be used to contact or identify you. Personally identifiable infornation may include, but is not limited to your NAME, EMAIL ADDRESS, PHONE NUMBER, ANY INFORMATION YOU INCLUDE IN THE CONTENTS OF THE MESSAGES.
For more information, please send an Marco's Backyard Swimming an email
Pier Solutions is the CREATOR of "www.marcosbackyardswimming.ca" and is liable for none of the actions or decisions made on behalf of Marco's Backyard Swimming or anyone in any operation or control of Marco's Backyard Swimming


The CSS box model is the box that every HTML element is contained in. Every box is composed of four parts: Content, padding, border and margin. Understanding what these properties are and how to use them are important for creating desired layouts.
The content is the text/image/video. In the example below I have two elements. One contains the text 'Content' which will be modified with padding, border and margin, and the other with the text 'Same size as the content box' that will remain the same to allow observations of the changes that will be made.
Padding clears a transparent area around the content. Length (px, pt etc.) percentage values or inherited values from a parent element are used to specify the property. In the example below 90px padding has been added. Padding is included in the total width of the element, and the difference can be observed below with the ‘content’ box in comparison to the second box.
Padding properties can be further specified to sides of the element using padding-top, padding-left, padding-bottom, padding right. The content box below has been modified to display 90px padding-bottom.
Border goes around the padding and content area. It specifies the border color, style, and width using the properties border-color, border-style and border width. Borders are also included in the overall size of the element.
Margin clears a transparent area around the border, it is used to seperate from neighbouring elements. The values for this property are length (px, pt, cm, etc.), percentage, auto or inherited from a parent element.
Margin sides can be specified with margin-top, margin-left, margin-bottom, and margin-right. The example below has a 50px margin at the bottom. It is important to note that if the second box had a margin value as well, the total margin value will not be the two values added. The larger value will determine the size of the margin. Margins are not included in the total size of the element.


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@Copyright 2017 @ Julian lee


Static-Bliss¶ ↑
A gem for modularizing Jekyll-built website updates and pushing to an s3 bucket.
Requirements¶ ↑
Gem requirements (Depending on what access abilities you want)
s3 aws-sdk google_drive
Directory Requirements¶ ↑
A _data
folder at the root of your site will hold the required
Configuration¶ ↑
Modify your _config.yml
file to include the following values:
-
google_info
Additionally, create another file called _secret_config.yml
with the following contents:
google_username<EMAIL_ADDRESS>google_password : "qwerty1" s3_id : "S3 ID" s3_secret : "S3 Secret" production_bucket: "yourbucketnamehere"
Be sure to add the following line to your .gitignore file:
_secret*.*
Installation¶ ↑
The easiest method is to add the following line to your
Gemfile
gem 'Static-Bliss', :git => 'git://github.com/jenningsanderson/Static-Bliss.git'
and run bundle install
Execution¶ ↑
If installed with bundler (recommended), then you have to execute with bundler:
bundle exec bliss
If successful, you should see the following (functions dependent on configuration)
Command: help args: [] Reading the _config.yml file Loading site_config from _config.yml Loading credentials from site_config location Welcome to Static-Bliss, a gem built to make updating your jekyll site very simple. Loading site_config from _config.yml Loading credentials from site_config location The following functions are available based on your configuration: bliss publish bliss update press bliss update people [all] bliss update people Current bliss update people Alumni bliss update projects bliss update publications bliss update all Note: Additional parameters for each of these functions may be available depending on your object classes
Remember to call bundle exec
before bliss
when
running the functions.


Ben Affleck, Gal Gadot Join Calls to Release Zack Snyder’s ‘Justice League’ Cut
by Genevieve ScaranoMany stars, including Ben Affleck and Gal Gadot, are urging Warner Bros. to release Zack Snyder’s cut of Justice League.
In 2017, Snyder, who previously worked on Batman v Superman: Dawn of Justice and Man of Steel, had to step away from Justice League due to a family tragedy, Slate.com reported. Joss Whedon took over Snyder’s role and completed the film’s production efforts, however, fans and celebrities want to see Snyder’s original cut of the movie, Entertainment Weekly noted.
On Sunday, Affleck and Gadot both tweeted #ReleaseTheSynderCut,” and joined thousands of fans calling for the original version of Justice League. DC actors Ray Fisher and Christina Wren also demanded the Snyder cut on their social media accounts.
Snyder also responded to the #ReleaseTheSynderCut movement and praised the stars and fans for their efforts.
“This ancient Amazonian can’t be wrong. Neither can Batman,” Snyder tweeted on Nov. 17.
Warner Bros. has not provided comment on the #ReleaseTheSnyderCut activity.
More on Geek.com:


{% include 'monitor/header.html' %} You have logged out Thank you for using AirQual {% include 'monitor/footer.html' %}
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Contact Gaurav Joshi!!
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M’sian Overcomes Rare Immune Disease That Almost Killed Her, & Now She’s a Masters Student
by Veronica ElankovanTap to listen to this article instead: 🔊 Listen to Post
Imagine having it all and then, one day everything is snatched away from you? It’s hard to even think about what that must feel like.
Adeleine Aelissa had to go through one of the worst experiences in her life after she was diagnosed with a very rare immune disease. It was on the 21st of July 2017 when Adeleine’s entire world came crashing down after her erratic behaviour spiralled out of control, which later landed her in the hospital.
A week prior, the pre-school teacher was down with a viral fever and she also had insomnia – a disorder where one has a hard time falling asleep. But, things worsened when she started developing peculiar behaviours which were beyond comprehension.
Everything went south when she was tossed in a psychotic abyss; and baffled and worried for their eldest daughter, her family then brought her to the Emergency Department of University Malaya Medical Centre (PPUM). She even put up a fight with her family when they wanted to bring her to the hospital.
And, that was it! Adeleine told WORLD OF BUZZ that beyond that episode, she remembers nothing. The whole ordeal was, later, narrated to her by her family. So, here’s how the story goes:
1. Adeleine was admitted into the psychiatric ward
Upon reaching the hospital, Adeleine said that she was out-of-control and the medical team tied her hands down because she was trying to escape. She shared: “I bit and pulled out my drips and feeding tubes several times.”
Since Adeleine’s disease was a rare one, the doctors couldn’t figure out her medical condition immediately but given her psychotic-like behaviour, the poor lady was admitted into the psychiatric ward. This was a little hard on her father as he works in the psychiatric ward, so seeing his little girl being admitted to the ward was heart-breaking.
2. A panel of specialist and doctors tried to diagnose her unfathomable disease
Following that, a panel of specialists and doctors teamed up to figure out Adeleine’s actual medical condition. So, they interviewed her elder brother about her most recent activities and habits. Several days passed by and the experts still couldn’t diagnose her condition. At this point, Adeleine was unconscious.
She had a high fever and a series of seizures at the beginning stage of her disease. Besides that, her family was told to prepare for the worst because she could be bed-ridden forever, or she could lose her life. Everything she had going on in life was put on hold, but thankfully, her workplace didn’t hire a new teacher to fill up her spot. They kept it open until she was fit to work again.
3. Her rare disease was finally diagnosed by medical experts
Her condition wasn’t getting any better but after consultation by family doctors, she underwent an LP (lumbar puncture). FYI, LP is a medical procedure where the cerebrospinal fluid (CSF) is collected for a test. They are normally conducted to help medical experts diagnose the central nervous system’s diseases.
In addition to the LP, she had a brain MRI test and a special blood test which detects antibodies that are targetting particular receptors in the brain. A few days later, Adeleine was diagnosed with anti-NMDA Receptor Encephalitis.
4. Encephalitis, the largely unknown and rare disease
Encephalitis (or brain inflammation) occurs when the patient’s immune system attacks the NMDA receptors in the brain. These receptors are proteins that control electrical impulses, and they are in charge of the following brain functions:
- Judgement
- Perception of reality
- Human interaction
- The formation and retrieval of memory
- The control of unconscious activities (like breathing and swallowing)
Once the immune system attacks NMDA receptors, the patients will suffer several changes in mood and behaviour. Some of them are mentioned below:
- Violent outbursts
- Paranoia
- Memory loss
- Speech problems
- Numbness
- Seizures
- Involuntary movements
- Increased heart rate
- Irregular heart rhythm
- Slowed breathing
- Decreased levels of consciousness
In some cases, patients can fall into an “unresponsive catatonic state” and it may last for weeks. In Adeleine’s case, it lasted for MONTHS.
5. Adeleine’s bumpy and thorny road to recovery
Her road to recovery wasn’t an easy one but her perseverance and strong will helped her fight through the obstacles. Doctors decided to put her on a higher dosage of medicines and she was put into an isolated ICU. Thus, only immediate family members could visit her, and they had to wear isolation gowns, masks and gloves to enter. It was to reduce the risk of infection.
Initially, they had to make an airway on her throat to ease her breathing, and it also acted as a suction pathway to get rid of excessive flu and phlegm. Additionally, Adeleine was on ventilators because she couldn’t breathe properly by herself.
A temporary pacemaker was also implanted to treat her irregular heartbeats, but it was removed a week later. Then, she went through five tests – three MRIs and two CT scans – to help diagnose other conditions like seizures, epilepsy and etc.
That wasn’t all as the resilient now-26-year-old underwent 12 plasma exchange procedures (Plasmapheresis – a process to clean the blood). She was strapped to a feeding tube and only ate liquid food. As she was getting better, Adeleine was transferred to the rehabilitation ward.
Even though she was recovering, Adeleine had lost her complete memory – meaning she doesn’t remember whatever that had happened several months prior to her attack. She was still talking, but she couldn’t write; and oftentimes, she would also prefer to left alone because she didn’t enjoy the company of people even though she was an extroverted person.
6. Her road to recovery
Hence, Adeleine went through physiotherapy and other programs to recover her memory, including her brain and muscle memory. While she was in the hospital, her elder brother made sure that she completed several exercises to refresh basic memories, like her best friends and her favourite music director. Here’s an example of that exercise:
The exercise above was designed to help her exercise her memory because, during recovery, she was often forgetful. Three months later, she was out of the hospital, but she still attended physiotherapy and occupational therapy every week.
These therapies helped her cognitive skills and helped her regain skills like driving & typing.
Adeleine told WORLD OF BUZZ,
“I was no longer fit and that was my biggest challenge. I had no physical strength and energy. This affected my left hand/arm because the blood pressure monitor was fixed on my left arm.”
“My only consolation was my family and for that, I am extremely grateful.”
With all the support from her family and friends, Adeleine stands tall today like the warrior she is. After two years, Adeleine is now back on her feet and nothing is slowing her down because she is living her best life yet.
The warrior resumed her previous job as a pre-school teacher at Julia Gabriel and was recently awarded Ms Chiltern House for her dedication towards her job. Amazing!
Currently, she’s a Master of Education student at UNITAR International University, and she’s doing pretty well. Rest assured, Adeleine is glad that she made it through the storm. She, finally, told us,
“I got through what I thought I wouldn’t survive.  And, I am glad that I have survived this battle. A fighter never gives up.”
We are extremely proud and ecstatic that Adeleine defied all odds and emerged victorious from her battle. She reminds us every day to never give up and always fight. To Adeleine: We hope that you’ll achieve all your hearts’ desire and hopefully, you will remain an inspiration to every Malaysian out there. You go, girl!
Also read: 19yo Hijab-Wearing Malaysian Girl Beats 4 Men and Wins Wrestling Championship


Dash UI Library
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undo all changes
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to edit this page go to 'partials/greet.html'
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Using Jupyter notebooks in Sphinx¶
Jupyter notebooks can be included in Sphinx documents using the nbsphinx extension
sudo -H pip3 install nbsphinx
Once installed, nbspinx needs to be added to the extensions section of the conf.py file. It is also a good idea to add **.ipynb_checkpoints to the exclude_patterns section.
extensions = ['nbsphinx']
exclude_patterns = ['_build', '**.ipynb_checkpoints']
The program pandoc also needs to be installed for this to work
Now you can add your .ipynb files to your Sphinx project


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