Augustin Luna cannin

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National Library of Medicine & National Cancer Institute
Bethesda, MD, USA
https://www.linkedin.com/in/augustin-luna
@canninl
in/augustin-luna

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cannin / causalpath_total_protein_example_large_nodes.format

Last active January 16, 2024 06:37

Description of CausalPath .format files

	# COLUMNS: For entries "all-nodes and color": obj_type all-nodes obj_subtype color
	# COLUMNS: For entries "all-nodes and bordercolor": obj_type all-nodes obj_subtype color
	# COLUMNS: For entries "node and color": obj_type node_label obj_subtype color
	# COLUMNS: For entries "node and rppasite": obj_type node_label obj_subtype subtype_info\|subtype_label\|subtype_bkgrd_color\|subtype_border_color
	# COLUMNS: For entries "node and tooltip": obj_type node_label obj_subtype tooltip_information_onmousehover
	# NOTE: "subtype_info" is also tooltip information for onmousehover for individual rppasite
	node all-nodes color 255 255 255
	node all-nodes bordercolor 50 50 50
	node FOXA1 color 40 80 255
	node FOXA1 tooltip FOXA1, -24.349700502698532

cannin / data_causalpath.txt

Last active July 8, 2021 16:58

CausalPath Input Files for GPVI Mass Spectrometry Dataset (Use with CausalPath 1.2.0)

	ID Symbols Sites Effect SignedP RF1_tmm RF3_tmm RM1_tmm RM2_tmm RM4_tmm AF1_tmm AF3_tmm AM1_tmm AM2_tmm AM4_tmm
	FCER1G_Y58 FCER1G Y58 2.11849506973498e-05 14373.7574077909 22647.2457028369 16986.5946283221 27719.8497871752 25761.9333453212 330396.455874962 414293.146733761 274970.966990486 424255.557710368 424831.777807267
	KIF13B_S1410 KIF13B S1410 -3.38001049753508e-05 222427.345933258 408896.243632753 536178.803602148 265699.614247014 315299.651610471 33008.9300818369 61839.5888539012 76572.8891839867 50171.5952669212 57210.6794113786
	PPFIA1_S763 PPFIA1 S763 -3.38001049753508e-05 260733.273908766 260643.546811825 301800.661843004 269186.980592221 264805.096994688 58042.0671941481 58707.2094650245 67105.7372397264 67267.703407248 68742.5910655683
	ERC1_S21 ERC1 S21 -3.40790075308345e-05 425882.416218268 473500.960254598 516485.607088445 420746.036892043 509023.952492173 93774.4387777743 99406.0045636096 108523.096047869 103967.484242926 130837.499972744
	FCER1G_T66 FCER1G T66 4.38968506191598e-05 72383.74

cannin / transport.txt

Created May 10, 2021 19:11

BioPAX L3 Transport Example

	// From: https://www.pathwaycommons.org/archives/PC2/v12/PathwayCommons12.pid.BIOPAX.owl
	// NOTE: Removed some evidence, comments, datasources, xrefs

	<bp:Transport rdf:ID="Transport_e5c5c3064a35275da036764754d82987">
	<bp:participantStoichiometry rdf:resource="#Stoichiometry_c62e952f57267e590061a656114147e6" />
	<bp:participantStoichiometry rdf:resource="#Stoichiometry_35daf0896d936055fc0ce682622172f4" />
	<bp:xref rdf:resource="http://identifiers.org/pubmed/11756469" />
	<bp:right rdf:resource="#Protein_cbbdfcd1f7535c5e7d154b9a7d49a428" />
	<bp:left rdf:resource="#Protein_c9661c9e4c9789d8d328a723f626a460" />
	<bp:comment rdf:datatype = "http://www.w3.org/2001/XMLSchema#string">REPLACED http://pathwaycommons.org/pc12/Transport_e5c5c3064a35275da036764754d82987</bp:comment>

cannin / ish_apk_installation.md

Last active January 21, 2021 16:59

iSH apk Installation Instructions

cat /dev/location > /dev/null &

cd 
wget http://dl-cdn.alpinelinux.org/alpine/latest-stable/main/x86/apk-tools-static-2.10.5-r1.apk
cd /
tar xvzf ~/apk-tools-static-2.10.5-r1.apk
ln -s /sbin/apk.static /sbin/apk
cd
apk

cannin / pyenv_installation_notes.md

Last active March 12, 2021 20:37

Installation Notes for pyenv to Support Reticulate and Seaborn

Parameters

--enable-shared for reticulate
--with-tcltk for seaborn

CONFIGURE_OPTS="--enable-shared --with-tcl-tk" pyenv install 3.8.1 # Needed separately? 

env \
  PATH="$(brew --prefix tcl-tk)/bin:$PATH" \
 LDFLAGS="-L$(brew --prefix tcl-tk)/lib" \

cannin / Pipfile

Created November 24, 2020 14:11

Use JSONPath in R with R reticulate and the jsonpath-ng Python package

	[[source]]
	url = "https://pypi.org/simple"
	verify_ssl = true
	name = "pypi"

	[dev-packages]
	ipython = "*"

	[packages]
	jsonpath-ng = "*"

cannin / new_issue_template_factoid.md

Created September 3, 2020 17:23

new_issue_template_factoid

Description

Q: What is the name of the feature?

Q: What does this feature enable the user to do?

cannin / cbioportal_installation_notes.txt

Last active July 9, 2020 17:40

cBioPortal Installation Notes

	# Network
	docker network create cbionet

	# MySQL
	docker rm -f cbiodb; docker run -d --restart=always \
	--name=cbiodb \
	--network=cbionet \
	-e MYSQL_ROOT_PASSWORD='P@ssword1' \
	-e MYSQL_USER='cbio' \
	-e MYSQL_PASSWORD='P@ssword1' \

cannin / pmc_journal_list_20200113.txt

Last active June 26, 2020 12:08

1) Number of Interactions Per Journal for REACH Dataset and 2) List of PMC Journals

	journal
	... Int Conf Ind Instrum Control
	""
	"Cell Biol (Henderson, NV)"
	"Cellbio (Irvine, Calif)"
	"Clin Biomech (Bristol, Avon)"
	"Identity (Mahwah, N J)"
	"J Environ Prot (Irvine, Calif)"
	"Psychobiology (Austin, Tex)"
	"Res Rep (Montgomery, Ala.)"

cannin / userscripts_linkedin_pubmed_entry.user.js

Last active June 22, 2020 03:28

LinkedIn PubMed and DOI Entry: (NOT WORKING, https://userscripts-mirror.org/scripts/review/95938)

	// ==UserScript==
	// @name LinkedIn PubMed Entry
	// @namespace http://alternateallele.com
	// @version 1.3.1
	// @description Populate LinkedIn's publication page with a PubMed ID.
	// @include http://www.linkedin.com/profile/edit*
	// @require http://ajax.googleapis.com/ajax/libs/jquery/1.3.2/jquery.min.js
	// @grant GM_xmlhttpRequest
	// ==/UserScript==

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