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diff --git a/tools/sage.csv b/tools/sage.csv new file mode 100644 index 00000000..01ee8017 --- /dev/null +++ b/tools/sage.csv @@ -0,0 +1,166 @@ +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,,
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