NML Bioinformatics ServiceLicensed Bioinformatics Tools High-throughput Data Analysis

NML Bioinformatics ServiceLicensed Bioinformatics Tools High-throughput Data Analysis Vector NTI Advance Literature Study Data Mining Functional Genomics Analysis Cumulative Annual Registered Users of NML Licensed Commercial Bioinformatics Resources Software License type License number Open Access 2013 2014 Unlimited 15 24 Annual/Floating 6 42 68 Nextbio Annual/Site Unlimited 230 278 318 333 BIOBASE Annual/Site Unlimited 154 226 289 316

Oncomine* Annual/Named 1 40 53 56 63 Golden Helix SVS 7** Annual/Floating 1 7 18 24 Genevestigator Annual/Named 10 17 19 21 28 Partek Genomics Suite Annual/Floating 2 61 78 101 137 165 204 225 Ingenuity Pathway Analysis Annual/Floating 3 102

131 243 308 401 498 553 Perpetual/Floating 2 33 67 79 88 103 115 242 411 972 1248 1570 1725 Galaxy Partek Flow Vector NTI Advance Total Annual Registered Users 2008 163 2009 2010 2011 2012 * Oncomine was downsized to 2 named users starting FY2014, user growth in 2014 represent the number of consultation requests ** Golden Helix SVS 7 was downsized from 1 floating license to 1 fixed license starting FY2014 and discontinued in FY2015 Centralized Licensing Model Delivers Dramatic Cost Saving Licensing cost comparison of IPA licensing based on 170 active USC users in 2014

University license Individual license $65,000 $1,870,000 600 Jan12 Feb -12 Mar -12 Apr -12 May -12 Jun12 Jul12 Aug -12 Sep -12 Oct -12 Nov -12 Dec -12 Jan13 F eb -13 Mar -13 Apr -13 May -13 Jun13 Jul13 Aug -13 S ep -13 Oct -13 Nov - 13 Dec -13 Jan14 Feb -14 Mar -14 Apr -14 May -14 Jun14 Jul14 Aug -14 Sep -14 Oct

-14 Nov -14 Dec -14 Number of Sessions 700 Average monthly sessions = 314 Average monthly hours = 323 hr 100 0 700 500 600 500 400 400 300 300 200 200 100 0 Number of Hours Ingenuity Pathway Analysis Usage @ USC (Jan. 2012-Dec.2014) 800 Ingenuity Pathway Analysis Monthly Denied Sessions (Jan. 2013-Nov. 2014) 300 Average monthly denied sessions = 117 250 200 150 100 50 / 01 13 / 02 13 / 03

13 / 04 13 / 05 13 / 06 13 / 07 13 / 08 13 / 09 13 / 10 13 / 11 13 / 12 13 / 01 14 / 02 14 / 03 14 / 04 14

/ 05 14 / 06 14 / 07 14 / 08 14 / 09 14 / 10 14 11 / 0 14 Bioinformatics Computing Resources at Norris Medical Library Computer Workstations in Norris Medical Library Hardware: Four Dell Precision T3550/T3660 workstations with 6-core Intel Xeon processors, 2432GB memory Software: Partek Flow, Galaxy, Cistrome, annovar R& Bioconductor, CAP-miRSeq Total Storage: 62 TB (May 2015) Custom Computing Cluster in USC HighPerformance Computing Hardware: One head node and 9 worker nodes*. Each with dual processor 6/8-core AMD Opteron 6176 or Intel E5-2650, 48-64 GB memory. Software: Partek Flow, Galaxy, Cistrome, R& Bioconductor Total Storage: 4 TB HPC file system Log on HPC Yo u HPC-NML head node HPC-NML custom condo 2014 Next Generation Sequencing (NGS)

Data Analysis at NML Bioinformatics Service Partek Flow From To # Users # Projects # Data Files Total Raw File Size (GB) Total Run Time (day) 1/1/2014 12/31/2014 46 236 2608 9901 549.5 Galaxy From To # Users # Projects # Data Files Total Raw File Size (GB) Estimated Run Time (day) 1/1/2014 12/31/2014 10 30 338 454 38 NGS Growth in Biomedical Research 50000 2500

45000 40000 2000 35000 30000 1500 25000 20000 1000 15000 10000 500 5000 0 2010 2011 GEO - 2012 2013 Pubmed - 2014 0 Computing Storage Growth at NML Bioinformatics Service Total Storage (TB) 70 62 60 50 38 40 30 22 20 10 0 4 2012 2013 2014 2015