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add bio gpu demos #509

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add bio gpu demos #509

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d2b9f02
add cpu bio-demos
dcolinmorgan Jul 19, 2023
faf1c6b
add gpu bio demos
dcolinmorgan Jul 19, 2023
f54f8e8
update metagenomic demo
dcolinmorgan Jul 26, 2023
8407501
updated sc demo for gene name clusters
dcolinmorgan Jul 27, 2023
6605e76
fixed pre-gpu link
dcolinmorgan Aug 8, 2023
9c1b548
add cpu bio-demos
dcolinmorgan Jul 19, 2023
626efa0
add gpu bio demos
dcolinmorgan Jul 19, 2023
299292f
update metagenomic demo
dcolinmorgan Jul 26, 2023
5b97dfe
updated sc demo for gene name clusters
dcolinmorgan Jul 27, 2023
7e499fb
fixed pre-gpu link
dcolinmorgan Aug 8, 2023
4f796d7
Merge branch 'bio-demos' of https://github.com/graphistry/pygraphistr…
dcolinmorgan Nov 23, 2023
11fff49
Merge branch 'master' into bio-demos
dcolinmorgan Jul 3, 2024
609b383
update url and import nrows
dcolinmorgan Jul 5, 2024
e3efbc5
ST attempt1
dcolinmorgan Jul 5, 2024
74ebf7c
ST attempt2
dcolinmorgan Jul 5, 2024
df92d58
isnt ST req from base
dcolinmorgan Jul 5, 2024
4b45c6a
isnt ST req from base
dcolinmorgan Jul 5, 2024
eef1d6d
update links and plots, etc
dcolinmorgan Jul 9, 2024
e7f784e
backout ST import try
dcolinmorgan Jul 10, 2024
5adad4b
backout proper
dcolinmorgan Jul 10, 2024
7ad581c
revised demos
dcolinmorgan Jul 11, 2024
0c7ada6
2nd meeting fixes partial, no readme update
dcolinmorgan Jul 15, 2024
e75a38c
add biogrid notebook to gallery grid
dcolinmorgan Jul 16, 2024
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191 changes: 66 additions & 125 deletions ...s/demos_by_use_case/bio/BiogridDemo.ipynb → ...mos_by_use_case/bio/cpu/BiogridDemo.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@
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"execution_count": 3,
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Expand All @@ -48,26 +48,26 @@
"name": "stderr",
"output_type": "stream",
"text": [
"/usr/local/lib/python2.7/site-packages/IPython/core/interactiveshell.py:2717: DtypeWarning: Columns (19,20) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" interactivity=interactivity, compiler=compiler, result=result)\n"
"/var/folders/sx/x954rbdd44d932dd0ygfp1qc0000gn/T/ipykernel_51237/4214251102.py:2: DtypeWarning: Columns (19,20) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" rawdata = pandas.read_table(url1, na_values=['-'], engine='c')#, compression='gzip')\n"
]
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Expand Down Expand Up @@ -134,14 +134,14 @@
"2 Wang T (1996) Low Throughput "
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"metadata": {},
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"source": [
"url1 = 'https://s3-us-west-1.amazonaws.com/graphistry.demo.data/BIOGRID-ALL-3.3.123.tab2.txt.gz'\n",
"rawdata = pandas.read_table(url1, na_values=['-'], engine='c', compression='gzip')\n",
"url1 = 'http://thebiogrid.org/downloads/archives/Release%20Archive/BIOGRID-3.3.123/BIOGRID-ALL-3.3.123.tab2.zip'\n",
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https

"rawdata = pandas.read_table(url1, na_values=['-'], engine='c')#, compression='gzip')\n",
"\n",
"# If using local data, comment the two lines above and uncomment the line below\n",
"# pandas.read_table('./data/BIOGRID-ALL-3.3.123.tab2.txt', na_values=['-'], engine='c')\n",
Expand All @@ -162,35 +162,9 @@
},
{
"cell_type": "code",
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"execution_count": null,
"metadata": {},
"outputs": [
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{
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"\n",
" <iframe id=\"59e1c841-c0e5-4b53-a0f7-29650ec2536f\" src=\"https://hub.graphistry.com/graph/graph.html?dataset=s3://graphistry.data/pygraphistry/50ad94358da9e7cb7924335eb336ce7a/dataset.json&type=jsonMeta&viztoken=081a2c85d68a5d175fdf33fe29297ed6fe724c99&usertag=86f11264-pygraphistry-0.9.63&splashAfter=1554614704&info=true\"\n",
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],
"outputs": [],
"source": [
"g = graphistry.bind(source=\"BioGRID ID Interactor A\", destination=\"BioGRID ID Interactor B\")\n",
"g.plot(interactions.sample(10000))"
Expand All @@ -206,7 +180,7 @@
},
{
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"execution_count": 9,
"metadata": {
"scrolled": true
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Expand All @@ -215,18 +189,18 @@
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Expand Down Expand Up @@ -263,15 +237,15 @@
"22 3 Arabidopsis thaliana"
]
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"execution_count": 4,
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# This downloads 170 MB, it might take some time.\n",
"url2 = 'https://s3-us-west-1.amazonaws.com/graphistry.demo.data/BIOGRID-IDENTIFIERS-3.3.123.tab.txt.gz'\n",
"raw_proteins = pandas.read_table(url2, na_values=['-'], engine='c', compression='gzip')\n",
"url2 = 'http://thebiogrid.org/downloads/archives/Release%20Archive/BIOGRID-3.3.123/BIOGRID-IDENTIFIERS-3.3.123.tab.zip'\n",
"raw_proteins = pandas.read_table(url2, na_values=['-'], skiprows=28)#, engine='c', compression='gzip')\n",
"\n",
"# If using local data, comment the two lines above and uncomment the line below\n",
"# raw_proteins = pandas.read_table('./data/BIOGRID-IDENTIFIERS-3.3.123.tab.txt', na_values=['-'], engine='c')\n",
Expand All @@ -291,7 +265,7 @@
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Expand All @@ -300,18 +274,18 @@
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Expand Down Expand Up @@ -348,7 +322,7 @@
"2 106605 ACVR1"
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Expand All @@ -375,25 +349,25 @@
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Expand Down Expand Up @@ -434,7 +408,7 @@
"2 106605 ACVR1 Homo sapiens"
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Expand All @@ -453,7 +427,7 @@
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Expand All @@ -470,25 +444,25 @@
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Expand Down Expand Up @@ -538,7 +512,7 @@
"2 Homo sapiens 0 "
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Expand All @@ -557,7 +531,7 @@
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Expand All @@ -566,18 +540,18 @@
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Expand Down Expand Up @@ -649,7 +623,7 @@
"2 Low Throughput "
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"execution_count": 9,
"execution_count": 14,
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Expand All @@ -673,44 +647,11 @@
},
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"metadata": {
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{
"name": "stdout",
"output_type": "stream",
"text": [
"Uploading 7139 kB. This may take a while...\n"
]
},
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"data": {
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"\n",
" <iframe id=\"083451dc-af48-4258-8c35-74f97130ea2e\" src=\"https://hub.graphistry.com/graph/graph.html?dataset=s3://graphistry.data/pygraphistry/7b876012458fc4c83644f88b14f96be5/dataset.json&type=jsonMeta&viztoken=0db9e5e57bbe115a40b64692dd5f2d7a5f2ec4a0&usertag=86f11264-pygraphistry-0.9.63&splashAfter=1554614820&info=true\"\n",
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"execution_count": 10,
"metadata": {},
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],
"outputs": [],
"source": [
"# This will upload ~10MB of data, be patient!\n",
"g2 = g.bind(node='BIOGRID_ID', edge_title='Author', point_title='SYMBOL', point_color='Color')\n",
Expand Down Expand Up @@ -743,7 +684,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.11"
"version": "3.12.2"
}
},
"nbformat": 4,
Expand Down
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