mv sage code artifacts under domain/sage

3 files changed, 0 insertions, 167 deletions

diff --git a/tools/sage_csv_to_sage_json.py b/src/local/domain/sage/sage_csv_to_sage_json.py
index b89670ab..b89670ab 100755
--- a/tools/sage_csv_to_sage_json.py
+++ b/src/local/domain/sage/sage_csv_to_sage_json.py
diff --git a/tools/sage.csv b/tools/sage.csv
deleted file mode 100644
index 01ee8017..00000000
--- a/tools/sage.csv
+++ /dev/null
@@ -1,166 +0,0 @@
-id,name,dependent on
-1,Kick-off meeting,
-2,Definition of project plan,
-3,Definition of roles and responsibilities,
-4,Agreement on Data sharing modalities,
-5,,
-6,Aim 1 - Screen drugs against merlin-deficient VS and M cells,
-7,Final list of compounds ready,
-8,Assemble 20 to 40 drugs panel,
-9,Drugs in hands,8
-10,QC check on purchased drugs,9
-11,MTA negotiation with companies to secure drug supply,
-12,"Assemble, test growth rates and choose hum Upfront meningioma lines for M screening set ",
-13,Assemble pairs of lines for VS screening set (total 8 lines) Upfront,
-14,Optimize assay conditions,
-15,Primary Screening of 20 to 40 drugs against both M and VS,"14,11,9"
-16,Analysis of data from primary screening,15
-17,Upload of primary screening data into Synapse and report,16
-18,Secondary screening (independent Human M and VS lines) of top drugs,17
-19,Analysis of secondary screening data from secondary screening and interpretation,18
-20,Upload of data into Synapse and reporting - Identification report of active single agents,19
-21,Primary screening of drug combination,"17,58"
-22,Upload of primary screening of combination data into report Synapse and reporting,21
-23,Secondary screening of drug combination,"57,21"
-24,Upload of secondary screening data into Synapse and report - reporting,23
-25,Selection of drug(s)/Combination(s) for invivo screening,23
-26,Analysis of Human vs Mouse cell lines and selection of winner cell line for NCATS screen,"18,58,60,62"
-27,Selection of 'winner' cell line,"26,64"
-28,NCATS screening ,27
-29,NCATS hit evaluation,28
-30,Upload of data into Synapse and reporting,29
-31,NCATS hits in primary (or secondary?) screening panels (?),30
-32,Upload of data into Synapse and reporting,31
-33,,
-34,,
-35,Aim 2 - Collect and Integrate molecular System data to define targets and improve models,
-36,Exome/RNA analysis of human NF2-associated tumor at Novartis,"13,12"
-37,First deposition of data into the Cancer Cell Line Encyclopedia,36
-38,Report on Novartis's activities at project's meetings,36
-39,Report on Novartis's activities at project's meetings,36
-40,Report on Novartis's activities at project's meetings,36
-41,Report on Novartis's activities at project's meetings,36
-42,Report on Novartis's activities at project's meetings,36
-43,,
-44,Availability of data from DoD program at Gusella Lab on Exome scanning and RNAseq of Schwannomas and Meningiomas and upload on Synapse,
-45,Upload of consortium members pre-existing data into Synapse,
-46,Upload of publicly available data into the Synapse,"44, 45"
-47,Transcriptome profile of untreated cell lines (baseline analysis),"12,13"
-48,Upload Cell lines baseline characterization only,"13, 47"
-49,Transcriptome profile of screening lines control vs treated/responders,17
-50,Upload Control vs treated/responsers,49
-51,Transcriptome profile of screening lines control vs treated/responders of drug combination,"49, 24"
-52,Upload Control vs combination's responders,51
-53,Report on transcriptome profiling,52
-54,Jumping Library analysis of structural genomic changes in screening set lines,"12,13"
-55,Report on Jumping Library analysis,54
-56,TC call to decide first 6 cell lines to analyse,
-57,Kinome analysis of cell lines for baseline characterization ,"56,12,13"
-58,Upload of data into Synapse and reporting,57
-59,Kinome analysis of single agent drug responding cell lines,17
-60,Upload of data of single agent drug responding cell lines into Synapse,59
-61,Kinome analysis of combination of drugs responding cell lines,24
-62,Upload of data of combination of drugs responding cell lines into Synapse,61
-63,Report of both single agent and combination responders cell lines,"59, 62"
-64,Analysis of integrated system data,"44,37,46,51"
-65,Report on analysis of integrated system data - Generate report a list of proposed new targets,"64,68,70"
-66,"Target (genes, pathways) validation by shRNA",58
-67,Report on ongoing activities,66
-68,Final Report - ID of new targets for NF2,66
-69,Screening of drugs against validated targets,68
-70,Upload of data into Synapse and reporting,69
-71,Develop CRISP/Cas modified NF2 mutant AC and SC lines,58
-72,Upload of data into Synapse and reporting,71
-73,Develop CRISPR/Cas modified lines bearing cooperating mutations,72
-74,Upload of data into Synapse and reporting,73
-75,Test CRISPR-Cas lines with active drug(s)/combination(s),22
-76,Upload of data into Synapse and reporting,75
-77,RNAseq of genetically mod lines,"65, 72"
-78,Upload of data into Synapse and reporting,77
-79,Creation of a new set of genetically-accurate screening panel for NF2,"75, 74"
-80,Kinome analysis of invivo tumors,90
-81,Upload of data into Synapse and reporting,80
-82,RNAseq analysis of invivo tumors,90
-83,Upload of data into Synapse and reporting,82
-84,,
-85,Aim 3 - Screen drugs invivo in genetically engineered mouse (VS) and xenograft (M) models,
-86,Breeding of PeriostinCre; nf2flox/flox mice,
-87,Report on first year activities,86
-88,Evaluation of single agent responders for animal studies,"50, 60"
-89,Test drug(s)/combination(s) in PeriostinCre; nf2flox/flox mice,"20,88,86"
-90,First invivo drug testing (treatment),89
-91,First invivo drug testing (statistics),90
-92,Upload of data into Synapse and reporting,91
-93,Evaluation of single agent responders for animal studies,"52, 62"
-94,First invivo combination drug testing (treatment),93
-95,First invivo combination drug testing (statistics),94
-96,Upload of data into Synapse and reporting,95
-97,Last invivo drug testing slot (treatment),
-98,Last invivo drug testing (statistics),"89, 97"
-99,Upload of data into Synapse and reporting,98
-100,Colony breeding and stereotactic transplantation studies,
-101,Report on first year activities,100
-102,Evaluation of single agent responsers for animal studies,88
-103,Test drug(s)/combination(s) in BenMen1 xenograft model,"100, 20, 10"
-104,First invivo drug testing,103
-105,Upload of data into Synapse and reporting,104
-106,Evaluation of single agent responders for animal studies,93
-107,First invivo drug testing,106
-108,Upload of data into Synapse and reporting,107
-109,Last invivo drug testing slot,103
-110,Upload of data into Synapse and reporting,109
-111,Prioritize drug(s) for NF2 clinical trials,"80, 82"
-112,Supply human tumors,
-113,Report on first year activities,112
-114,Report on second year activities,113
-115,Final report,112
-116,Supply human tumors to Novartis for transcriptome and exome analysis and generation of transplantable human,
-117,Analysis of human tumors from patients,
-118,Report on first year activities,116
-119,Report on second year activities,118
-120,Neuropathological assessment of mouse model tumors,89
-121,Upload of data into Synapse and Final Reporting,120
-122,Generation of transplantable human xenograft,116
-123,Model available to the community (???),122
-124,,
-125,Aim 4 - Identify at least 1 drug to move forward for a clinical trial,
-126,Evaluation and Design of potential clinical trial(s),111
-127,Clinical trial start,126
-128,,
-129,"Aim 5 - Data Sharing, Dissemination plan and management",
-130,Setting up of Synapse platform (website,
-131,Training of researchers for data input,130
-132,"Data deposition, integration and sharing",131
-133,Report on 1y activities,
-134,Report on 2y activities,133
-135,Final report,132
-136,,
-137,Project Group calls (bi-weekly),
-138,Group call: decision on drug panel,
-139,Group call: decision on first cell lines to investigate for kinome and transcriptome profile,
-140,Group call: pre-existing data on drugs or cell lines to be uploaded in Synapse,
-141,,
-142,,
-143,,
-144,Project Management,
-145,Synodos Meeting (kick-off),
-146,General management,145
-147,Synodos Meeting(NF conference),146
-148,Synodos Meeting (Ext Review committee),146
-149,First Year report,148
-150,Synodos Meeting(NF conference),146
-151,Synodos Meeting (Ext Review committee),146
-152,Second Year report,151
-153,Synodos Meeting(NF conference),146
-154,Synodos Meeting (Ext Review committee),146
-155,Final report,"154,146"
-156,,
-157,,
-158,,
-159,,
-160,,
-161,,
-162,,
-163,,
-164,,
-165,,
\ No newline at end of file
diff --git a/tools/sage.json b/tools/sage.json
deleted file mode 100644
index 63b9b39c..00000000
--- a/tools/sage.json
+++ /dev/null
@@ -1 +0,0 @@
-{"nodes": [{"status": "unknown", "end": 1514844000, "name": "Kick-off meeting", "start": 1514757600, "type": "deliverable", "id": "1"}, {"status": "unknown", "end": 1516831200, "name": "Definition of project plan", "start": 1515362400, "type": "deliverable", "id": "2"}, {"status": "waiting", "end": 1517349600, "name": "Definition of roles and responsibilities", "start": 1515967200, "type": "deliverable", "id": "3"}, {"status": "current", "end": 1517868000, "name": "Agreement on Data sharing modalities", "start": 1516572000, "type": "deliverable", "id": "4"}, {"status": "waiting", "end": 1518386400, "name": "", "start": 1517176800, "type": "deliverable", "id": "5"}, {"status": "current", "end": 1518904800, "name": "Aim 1 - Screen drugs against merlin-deficient VS and M cells", "start": 1517781600, "type": "deliverable", "id": "6"}, {"status": "done", "end": 1519423200, "name": "Final list of compounds ready", "start": 1518386400, "type": "deliverable", "id": "7"}, {"status": "unknown", "end": 1519941600, "name": "Assemble 20 to 40 drugs panel", "start": 1518991200, "type": "deliverable", "id": "8"}, {"status": "unknown", "end": 1520460000, "name": "Drugs in hands", "start": 1519596000, "type": "deliverable", "id": "9"}, {"status": "current", "end": 1520978400, "name": "QC check on purchased drugs", "start": 1520200800, "type": "deliverable", "id": "10"}, {"status": "current", "end": 1521496800, "name": "MTA negotiation with companies to secure drug supply", "start": 1520805600, "type": "deliverable", "id": "11"}, {"status": "waiting", "end": 1522011600, "name": "Assemble, test growth rates and choose hum Upfront meningioma lines for M screening set ", "start": 1521410400, "type": "deliverable", "id": "12"}, {"status": "done", "end": 1522530000, "name": "Assemble pairs of lines for VS screening set (total 8 lines) Upfront", "start": 1522011600, "type": "deliverable", "id": "13"}, {"status": "waiting", "end": 1523048400, "name": "Optimize assay conditions", "start": 1522616400, "type": "deliverable", "id": "14"}, {"status": "waiting", "end": 1523566800, "name": "Primary Screening of 20 to 40 drugs against both M and VS", "start": 1523221200, "type": "deliverable", "id": "15"}, {"status": "done", "end": 1524085200, "name": "Analysis of data from primary screening", "start": 1523826000, "type": "deliverable", "id": "16"}, {"status": "waiting", "end": 1524603600, "name": "Upload of primary screening data into Synapse and report", "start": 1524430800, "type": "deliverable", "id": "17"}, {"status": "current", "end": 1525122000, "name": "Secondary screening (independent Human M and VS lines) of top drugs", "start": 1525035600, "type": "deliverable", "id": "18"}, {"status": "done", "end": 1527109200, "name": "Analysis of secondary screening data from secondary screening and interpretation", "start": 1525640400, "type": "deliverable", "id": "19"}, {"status": "done", "end": 1527627600, "name": "Upload of data into Synapse and reporting - Identification 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