Ralf Stephan rwst
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rwst
/ general_binet
Last active
January 3, 2016 21:59
The general Binet form of the nth element of a binary recurrence over the integers is, given a(n) = c*a(n-1) + d*a(n-2).
The Pari code is blinding fast, dependent on precision. It can maybe jump in when a floating point result is sufficient. The Sage function gives an expression in square roots.
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| (Pari/GP) | |
| a(c,d,a0,a1,n)=my(r1,r2,s);s=sqrt(c^2+4*d);r1=2*d/(-c+s);r2=2*d/(-c-s);return(((a1-c*a0+a0*r1)*r1^n-(a1-c*a0+a0*r2)*r2^n)/s) | |
| (Sage) | |
| def a(c,d,a0,a1,n): | |
| r1=2*d/(-c+sqrt(c^2+4*d)) | |
| r2=2*d/(-c-sqrt(c^2+4*d)) |
rwst
/ patchbot-13282-log.txt
Created
May 4, 2014 14:56
infinite loop when testing sage-patchbot with ticket 13282
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| Forcing sage-location, probably because a new package was installed. | |
| Updating various hardcoded paths... | |
| (Please wait at most a few minutes.) | |
| DO NOT INTERRUPT THIS. | |
| Done updating paths. | |
| Found package ccache in /scratch/sage/upstream/ccache-3.1.9.spkg | |
| Package ccache-3.1.9 is already installed. | |
| Use 'sage -f /scratch/sage/upstream/ccache-3.1.9.spkg' to force a reinstallation. | |
| --2014-05-04 08:27:25-- http://coates.ma.ic.ac.uk/grdb_polytopes-0.1.spkg | |
| Resolving coates.ma.ic.ac.uk (coates.ma.ic.ac.uk)... 155.198.35.88 |
rwst
/ piranha-degree.cpp
Created
November 16, 2015 08:17
benchmark program, compile with g++ -O0 -std=c++11 piranha-degree.cpp -lgmp -lmpfr -lpthread
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| #define BENCHPRESS_CONFIG_MAIN | |
| #include <cstddef> | |
| #include <benchpress/benchpress.hpp> | |
| //#include "series-benchmark.h" | |
| #include <string> | |
| #include <iostream> | |
| #include <tuple> | |
| #include <type_traits> |
rwst
/ add-omim.py
Created
August 21, 2019 06:56
creating QuickStatement batches for missing claims on Wikidata objects about genes and their corresponding OMIM entries
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| from sys import * | |
| import csv | |
| reader = csv.DictReader(open('gene-entrezids.tab', 'r'), delimiter='\t') | |
| genes = {} | |
| for item in reader: | |
| gid = item.get('geneid') | |
| iturl = item.get('item') | |
| iturl = iturl[iturl.rfind('/')+1:] | |
| gitem = genes.get(gid) |
rwst
/ missing-gene-disease.py
Created
August 24, 2019 17:08
creates QS statements associating gene items with disease items, from WD and UniProt data
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| from sys import * | |
| import csv | |
| reader = csv.DictReader(open('gene-diseaseassoc.tab', 'r'), delimiter='\t') | |
| genes = {} | |
| for item in reader: | |
| iturl = item.get('item') | |
| it = iturl[iturl.rfind('/')+1:] | |
| disurl = item.get('dis') | |
| dis = disurl[disurl.rfind('/')+1:] |
rwst
/ enzfam-subclass.py
Created
September 28, 2019 13:12
creates QS subclass-of statements for Wikidata enzyme families, to create hierarchy
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| import csv | |
| from anytree import Node, find, findall, PreOrderIter, RenderTree, Resolver, AsciiStyle, ChildResolverError | |
| from sys import * | |
| class ECNode(Node): | |
| q = '' | |
| lab = '' | |
| tree = ECNode('Root') |
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| import csv | |
| from anytree import Node, find, findall, PreOrderIter, RenderTree, Resolver, AsciiStyle, ChildResolverError | |
| from sys import * | |
| class TCNode(Node): | |
| q = '' | |
| lab = '' | |
| print_missing_triples = False | |
| print_qs = True |
rwst
/ move-sitelinks.py
Last active
November 7, 2019 09:42
produces QS commands to move all sitelinks from a list of WD items to corresponding items
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| import csv | |
| from sys import * | |
| reader = csv.DictReader(open('genes-wikipedia.tab', 'r'), delimiter='\t') | |
| gqs = {} | |
| for item in reader: | |
| iturl = item.get('p') | |
| qit = iturl[iturl.rfind('/')+1:] | |
| lang = item.get('lang') | |
| lemma = item.get('lemma') |
rwst
/ gist:258cb717ed548210913803ea7577fb31
Created
February 17, 2021 17:02
wdtaxonomy -iS Q3516872 (molecular biology technique)
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| molecular biology technique (Q3516872) ↑ | |
| |-polymerase chain reaction (Q176996) | |
| |-cell-free protein synthesis (Q189030) | |
| |-Rapid amplification of cDNA ends (Q381434) | |
| |-SuperSAGE (Q826829) | |
| |-restriction fragment length polymorphism (Q857299) | |
| |-Tandem affinity purification (Q893051) | |
| |-DNA-DNA hybridization (Q900923) | |
| |-Chromatin immunoprecipitation (Q901026) | |
| |-Immunophenotyping (Q902926) |
rwst
/ gist:8b78842260faff8402a5a10fc33908a9
Created
February 17, 2021 17:05
wdtaxonomy -iS Q26879200 (biochemistry method)
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| biochemistry method (Q26879200) ↑↑ | |
| |-Bradford protein assay (Q247562) | |
| |-Serial analysis of gene expression (Q286721) | |
| |-Förster resonance energy transfer (Q367473) | |
| |-Bimolecular fluorescence complementation (Q863465) | |
| |-Electrophoretic mobility shift assay (Q903596) | |
| |-density gradient electrophoresis (Q1209472) | |
| |-Protein Misfolding Cyclic Amplification (Q2044394) | |
| |-perfusion culture (Q2070705) | |
| |-submersed fermentation (Q2361902) |