Cornelius Roemer corneliusroemer
corneliusroemer
/ postgresCustom2.json
Created
September 15, 2024 17:08
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| { | |
| "$schema": "https://lnav.org/schemas/format-v1.schema.json", | |
| "postgres2": { | |
| "regex": { | |
| "duration": { | |
| "pattern": "^(?<timestamp>\\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}\\.\\d{3} UTC) (?<ip>\\d+\\.\\d+\\.\\d+\\.\\d+)\\((?<port>\\d+)\\) (?<session_id>[^ ]+) (?<transaction_id>\\d+) (?<operation>[A-Z]+) ?(?<level>[A-Z]+)?: (?:duration: (?<dur>\\d+\\.\\d+) ms)?(?<body>.*)$" | |
| } | |
| }, | |
| "opid-field": "transaction_id", | |
| "level-field": "level", |
corneliusroemer
/ sitemap.txt
Created
August 29, 2024 01:30
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| https://pathoplexus.org/ | |
| https://pathoplexus.org/about | |
| https://pathoplexus.org/about/development-team | |
| https://pathoplexus.org/about/eb | |
| https://pathoplexus.org/about/faq | |
| https://pathoplexus.org/about/governance | |
| https://pathoplexus.org/about/governance/data-submission | |
| https://pathoplexus.org/about/governance/eb-guidelines | |
| https://pathoplexus.org/about/governance/minutes | |
| https://pathoplexus.org/about/governance/minutes/2024-08-12_PathoplexusEBmeeting.pdf |
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| // A Newick grammar based on the specification by Gary Olsen: available at | |
| // https://phylipweb.github.io/phylip/newick_doc.html The grammar does _not_ include the optional | |
| // comments as I have not figured out how to include them without adding a lot of `comment?` rules | |
| // to the grammar whick makes it very slow. | |
| grammar Newick; | |
| tree: descendantList rootLabel? branchLength? SEMI; | |
| descendantList: LPAREN subtree (COMMA subtree)* RPAREN; | |
| subtree: (descendantList internalNodeLabel? | leafLabel) branchLength?; |
corneliusroemer
/ constraint_detector.py
Created
December 17, 2023 11:31
Script to detect incompatible splits in two newick trees
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| import argparse | |
| from pprint import pp | |
| from Bio import Phylo | |
| def get_terminals(clade): | |
| return frozenset(terminal.name for terminal in clade.get_terminals()) | |
corneliusroemer
/ nearest_nodes.ndjson
Created
December 1, 2023 14:48
Test data to reproduce polars bug
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| {"seqName":"England/MILK-28D52E2/2021","nearestNodes":["B.1.617.2"]} | |
| {"seqName":"USA/CO-CDPHE-2102374275/2021","nearestNodes":["B.1.617.2"]} | |
| {"seqName":"Wales/PHWC-PGY3IH/2021","nearestNodes":["B.1.617.2"]} | |
| {"seqName":"Turkey/HSGM-F70/2021","nearestNodes":["B.1.617.2"]} | |
| {"seqName":"USA/WI-CDC-QDX31282160/2021","nearestNodes":["B.1.617.2"]} | |
| {"seqName":"Canada/ON-SHL-21-02331/2021","nearestNodes":["B.1.617.2"]} | |
| {"seqName":"France/BRE-IPP48628/2021","nearestNodes":["B.1.617.2"]} | |
| {"seqName":"USA/CA-CDC-LC0396661/2021","nearestNodes":["B.1.617.2"]} | |
| {"seqName":"France/OCC-HCL021227635901/2021","nearestNodes":["B.1.617.2"]} | |
| {"seqName":"env/Ukraine/80004/2023","nearestNodes":["NODE_0000637","XBB.1.9.1"]} |
corneliusroemer
/ auto-faculty-profile.py
Created
September 26, 2023 02:24
Automatically generate faculty profiles using pubmed abstracts and GPT-4, filtering papers for relevance based on author position
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| import argparse | |
| from math import e | |
| from Bio import Entrez | |
| import openai | |
| def search_latest_papers(faculty_name, source="Pubmed", num_papers=5): | |
| papers_info = [] | |
| if source == "Pubmed": | |
| Entrez.email = "YOUR_EMAIL@example.com" |
corneliusroemer
/ auto-faculty-profile.py
Created
September 25, 2023 23:40
Automatically generate faculty profiles using pubmed abstracts and GPT-4
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| import argparse | |
| from math import e | |
| from Bio import Entrez | |
| import openai | |
| def search_latest_papers(faculty_name, source="Pubmed", num_papers=5): | |
| abstracts = [] | |
| if source == "Pubmed": |
corneliusroemer
/ gist:3a1dc19e6aa3ab5c94a5ed832a4a2c8e
Created
August 8, 2023 14:22
21Ltree20230808
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| {"version":"v2","meta":{"title":"SARS-CoV-2 phylogeny","updated":"2023-08-08","build_url":"https://github.com/neherlab/nextclade_data_workflows","maintainers":[{"name":"Cornelius Roemer","url":"https://neherlab.org"},{"name":"Richard Neher","url":"https://neherlab.org"}],"display_defaults":{"color_by":"clade_membership","distance_measure":"div","map_triplicate":false,"branch_label":"clade","transmission_lines":false},"genome_annotations":{"E":{"end":26472,"seqid":"defaults/reference_seq.gb","start":26245,"strand":"+","type":"CDS"},"M":{"end":27191,"seqid":"defaults/reference_seq.gb","start":26523,"strand":"+","type":"CDS"},"N":{"end":29533,"seqid":"defaults/reference_seq.gb","start":28274,"strand":"+","type":"CDS"},"ORF1a":{"end":13468,"seqid":"defaults/reference_seq.gb","start":266,"strand":"+","type":"CDS"},"ORF1b":{"end":21555,"seqid":"defaults/reference_seq.gb","start":13468,"strand":"+","type":"CDS"},"ORF3a":{"end":26220,"seqid":"defaults/reference_seq.gb","start":25393,"strand":"+","type":"CDS"},"ORF6": |
corneliusroemer
/ bf42tree.json
Created
April 17, 2023 12:42
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| { "version": "v2", "meta": { "title": "Subtree with Japan\/PG-462868\/2023|EPI_ISL_17243060|2023-02-28 and 51 other uploaded samples", "description": "Dataset generated by [UShER web interface](https:\/\/genome.ucsc.edu\/cgi-bin\/hgPhyloPlace) using the [usher](https:\/\/github.com\/yatisht\/usher\/) program. If you have metadata you wish to display, you can now drag on a CSV file and it will be added into this view, [see here](https:\/\/docs.nextstrain.org\/projects\/auspice\/en\/latest\/advanced-functionality\/drag-drop-csv-tsv.html) for more info.", "panels": [ "tree", "entropy"] , "display_defaults": { "branch_label": "aa mutations", "color_by": "pango_lineage_usher"} , "colorings": [ { "key": "userOrOld", "title": "Sample type", "type": "categorical", "scale": [ [ "uploaded sample", "#CC0000"] , [ "GISAID and\/or public", "#000000"] ] } , { "key": "gt", "title": "Genotype", "type": "categorical"} , { "key": "pango_lineage", "title": "Pango lineage", "type": "categorical"} , { "key": "Nextstrain_clade", |
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| {"version":"v2","meta":{"title":"SARS-CoV-2 phylogeny","updated":"2023-03-22","build_url":"https://github.com/neherlab/nextclade_data_workflows","maintainers":[{"name":"Cornelius Roemer","url":"https://neherlab.org"},{"name":"Richard Neher","url":"https://neherlab.org"}],"display_defaults":{"color_by":"clade_membership","distance_measure":"div","map_triplicate":false,"branch_label":"clade","transmission_lines":false},"genome_annotations":{"nuc":{"end":29903,"start":1,"strand":"+","seqid":"defaults/reference_seq.gb","type":"source"},"E":{"end":26472,"seqid":"defaults/reference_seq.gb","start":26245,"strand":"+","type":"CDS"},"M":{"end":27191,"seqid":"defaults/reference_seq.gb","start":26523,"strand":"+","type":"CDS"},"N":{"end":29533,"seqid":"defaults/reference_seq.gb","start":28274,"strand":"+","type":"CDS"},"ORF1a":{"end":13468,"seqid":"defaults/reference_seq.gb","start":266,"strand":"+","type":"CDS"},"ORF1b":{"end":21555,"seqid":"defaults/reference_seq.gb","start":13468,"strand":"+","type":"CDS"},"ORF3a":{" |
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