2012-10-09T11:40:19-05:00 2011-12-31 911194016 CLARK NUBER PS 10900 NE 4TH STREET SUITE 1700 BELLEVUE WA 98004 990 2011-01-01 912003593 INSTITUTE FOR SYSTEMS BIOLOGY INST 2067321200 401 TERRY AVENUE N SEATTLE WA 98109 JAMES R LADD 2067321200 2012-10-01 1 SARA ELIZABETH J HYRE P00235495 4254544919 2012-10-03 2011 2016-02-24 21:20:13Z LEROY HOOD 401 TERRY AVENUE N SEATTLE WA 98109 41995141 0 X WWW.SYSTEMSBIOLOGY.ORG X 1999 WA USING THE SCIENCE OF SYSTEMS BIOLOGY TO PREDICT, PREVENT, AND CURE DISEASE. 12 11 335 13 139884 138884 39044471 23892848 17334852 15963894 544409 -1564540 623927 510521 57547659 38802723 0 0 0 0 24299984 21990516 0 0 226224 26420568 25600381 50720552 47590897 6827107 -8788174 56185035 45477682 34311967 32642788 21873068 12834894 X THE INSTITUTE FOR SYSTEMS BIOLOGY (ISB) IS A NON-PROFIT RESEARCH INSTITUTE FOUNDED IN SEATTLE IN 1999 TO ADVANCE A SYSTEMS (OR HOLISTIC AND CROSS-DISCIPLINARY) APPROACH TO SCIENCE; PERSONALIZED MEDICINE; GLOBAL HEALTH AND ENVIRONMENTAL SUSTAINABILITY; SCIENCE EDUCATION; AND THE PIONEERING AND INVENTION OF BIOLOGICAL AND TECHNOLOGICAL METHODS AND TOOLS. OUR MISSION STATEMENT IS: REVOLUTIONIZE SCIENCE, TRANSFORM HUMAN HEALTH, AND ENSURE ENVIRONMENTAL SUSTAINABILITY. 0 0 23695869 470877 BIOMOLECULAR RESEARCH: INSTITUTE FOR SYSTEMS BIOLOGY SCIENTISTS PUBLISHED 84 RESEARCH PAPERS IN PEER-REVIEWED JOURNALS IN 2011. RESEARCH TOPICS INCLUDED: GENOMICS, MICROFLUIDICS, PROTEOMICS, HIGH-THROUGHPUT COMPUTATION, SYSTEMS BIOLOGY APPLICATIONS, AND BIOINFORMATICS. 699457 233580 SCIENCE EDUCATION: ISB'S CENTER FOR INQUIRY SCIENCE (CIS) PROVIDES TRAINING FOR K-12 SCIENCE TEACHERS IN MORE THAN 30 DISTRICTS ACROSS WASHINGTON STATE THAT SERVE 45 PERCENT OF THE TOTAL STUDENT POPULATION IN THE STATE. CIS STAFF HAVE HOSTED MORE THAN 40 PROFESSIONAL DEVELOPMENT SESSIONS, SERVING 750 SCIENCE EDUCATORS OVER THE COURSE OF 120 WORKSHOP DAYS. IN 2011, CIS STAFF LED THE PLANNING OF THE NATIONAL SCIENCE TEACHERS ASSOCIATION CONFERENCE HOSTED IN SEATTLE THAT ENGAGED APPROXIMATELY 3000 SCIENCE TEACHERS. 11943789 15259437 UNIVERSITY OF LUXEMBOURG (UL) COLLABORATION CONTRACT: THIS IS A FIVE-YEAR PROJECT UTILIZING FUNDS SPENT DOMESTICALLY, IN WHICH THE INSTITUTE WILL: (1) COORDINATE AND PERFORM RESEARCH WORK ON TWO PRIMARY PROJECTS RELATED TO (A) PERSONAL GENOME SEQUENCING AND SYSTEMS GENETICS AND (B) PERSONAL BLOOD PROTEOMICS, RNA, AND PROGENITOR CELL ANALYSIS; (2) ASSIST UL WITH ESTABLISHING AND RECRUITING FACULTY FOR A CENTER FOR SYSTEMS BIOLOGY (CSB); AND (3) TRANSFER KNOWLEDGE ABOUT SYSTEMS BIOLOGY TO UL STAFF THROUGH MENTORING, STAFF EXCHANGES, AND RESEARCH COLLABORATIONS. ACCOMPLISHMENTS IN 2011 INCLUDED: (1) GRAND OPENING OF LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE; HELPED ORGANIZE INAUGURAL SYSTEMS BIOLOGY SYMPOSIUM; (2) WHOLE GENOME SEQUENCE ANALYSIS OF 36 PEDIGREES, REPRESENTING 7 DIFFERENT DISORDERS, INCLUDING HUNTINGTON'S DISEASE, EPILEPSY, BIPOLAR DISORDER, SPINAL MUSCULAR ATROPHY, ACL INJURY, ALTERNATING HEMIPLEGIA OF CHILDHOOLD, AND FANCONI ANEMIA; (3) WHOLE GENOME SEQUENCE OBTAINED FROM MORE THAN 300 INDIVIDUALS; (4) DEVELOPED SPECIFIC TARGETED PROTEOMICS ASSAYS FOR NEARLY ALL 20,000 HUMAN PROTEINS; (5) DEMONSTRATED THE POWER OF ORGAN-SPECIFIC BLOOD PROTEIN AND MICRORNA STRATEGY FOR DISEASE DIAGNOSTICS; AND (6) A TOTAL OF 66 PUBLICATIONS REPRESENTING ALL ASPECTS OF THE UL COLLABORATION, MANY OF WHICH INCLUDED CO-AUTHORS FROM LCSB. 36339115 1 1 0 1 0 0 0 0 0 1 1 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 102 0 1 335 1 1 1 0 0 0 0 0 0 0 0 0 X 12 11 1 0 0 0 0 0 0 1 1 0 0 1 1 1 1 1 1 1 1 0 WA CA X GARY C STREICHER 2067321200 401 TERRY AVENUE N SEATTLE WA 98109 ROGER PERLMUTTER MD PHD 1.00 X 0 0 0 GARRY MENZEL PHD 1.00 X 0 0 0 CHARLES L HIRSCH 1.00 X 0 0 0 WILLIAM K BOWES JR 1.00 X 0 0 0 THOMAS J CABLE 1.00 X 0 0 0 LOUIS G LANGE MD PHD 1.00 X X 0 0 0 DAVID A SABEY 2.00 X 0 0 0 MARK ASHIDA 1.00 X 0 0 0 ROBERT T NELSEN 1.00 X 0 0 0 LEROY HOOD MD PHD 84.00 X X 382509 0 31962 STEPHEN GRAHAM 1.00 X 0 0 0 DANIEL T LING 1.00 X 0 0 0 LEIGHTON READ 1.00 X 0 0 0 FREDERICK FRANK 1.00 X 0 0 0 JAMES R LADD 40.00 X 282420 0 37815 SHIRLEY MEINECKE 40.00 X 89855 0 15499 EE SISSY BOUCHARD EDD 60.00 X 96959 0 13797 DAVID GALAS PHD 60.00 X 298667 0 32079 JOHN AITCHISON PHD 40.00 X 180516 0 23524 JOSEPH H NADEAU PHD 50.00 X 297194 0 25601 CATHRYN CAMPBELL JD PHD 40.00 X 272688 0 32035 ILYA SHMULEVICH PHD 50.00 X 199363 0 38977 DIANE R ISONAKA 40.00 X 209231 0 20895 NITIN S BALIGA PHD 50.00 X 202956 0 29325 ALAN ADEREM PHD 80.00 X 116290 0 17683 2628648 0 319192 29 1 1 0 BN BUILDERS 2601 4TH AVENUE SUITE 350 SEATTLE WA 98121 GENERAL CONSTRUCTION 5394265 COMPLETE GENOMICS INC 2071 STIERLIN COURT MOUNTAIN VIEW CA 94043 GENOME SEQUENCING SERVICES 3395490 MORRISON & FOERSTER LLP 12531 HIGH BLUFF DRIVE SUITE 100 SAN DIEGO CA 92130 LEGAL SERVICES 310956 PERKINS WILL INC 1221 2ND AVENUE SUITE 200 SEATTLE WA 98101 ARCHITECTURAL SERVICES 138002 VECA ELECTRIC 5614 SEVENTH AVENUE S SEATTLE WA 98108 ELECTRICAL CONTRACTOR 136188 7 2000 21892329 1998519 23892848 LUXEMBOURG COLLABORATN 541700 15259437 15259437 LAB AND RESEARCH SRVCS 541700 470877 470877 SCIENCE EDUCATION 541900 233580 233580 15963894 167439 167439 211917 211917 1623695 1409890 213805 213805 139884 73921 50549 1782528 -1731979 -1731979 -1731979 COST REIMBURSEMENTS 900099 83899 83899 REBATE 900099 900 900 84799 38802723 15963894 139884 -1193903 X 1485609 728642 662823 94144 14362529 10080162 4287081 -4714 1438689 995254 442981 454 3442601 2425978 1002817 13806 1261088 854120 400787 6181 585781 3500 574470 7811 514876 11227 503649 144459 144459 119909 119909 210898 205623 5275 73999 13413 60586 908232 43515 860140 4577 376953 33312 343641 5555361 5138418 324609 92334 544476 395533 148409 534 351031 101515 249516 142485 126507 13686 2292 3489815 3295651 189318 4846 138251 138251 SUBCONTRACTS 5911793 5911793 SUPPLIES 3180863 3160435 20152 276 SHARED SERVICES 1964250 1937561 26689 FELLOWSHIPS 326246 234651 91595 1060703 642305 414715 3683 47590897 36339115 11025558 226224 70450 300 24611013 15963174 10253126 6721277 1848141 463030 37500 30000 671283 335641 666644 3274868 35487250 17374067 17160753 18113183 184845 187195 681280 389014 56185035 45477682 7173342 5229409 7401564 4208566 9387000 8865500 10350061 14339313 34311967 32642788 X 4764116 -980318 8437452 5143712 8671500 8671500 21873068 12834894 56185035 45477682 X -8788174 -250000 X 0 1 1 X 1 1 X 27760023 36067112 29351797 39044471 23892848 156116251 27760023 36067112 29351797 39044471 23892848 156116251 8073814 148042437 974479 892643 1256885 1075697 1062338 5262042 24340 19519 3976 20244 139884 207963 1585 140398 139147 383582 84799 749511 162335767 41028739 0.91200 0.90950 X SCHEDULE A, PART II, LINE 10, EXPLANATION OF OTHER INCOME: COST REIMBURSEMENTS RESTRICTED RESTRICTED RESTRICTED RESTRICTED RESTRICTED RESTRICTED RESTRICTED RESTRICTED 0 0 0 0 0 0 1 119909 0 0 119909 0 8671500 84324 84324 8671500 8671500 83055 83055 8671500 8671500 161549 161549 8671500 8671500 8671500 1.00000 0 0 14516820 1259412 13257408 20970430 16114655 4855775 18113183 DEFERRED RENT PAYABLE 14339313 14339313 38802723 47590897 -8788174 -250000 -250000 -9038174 39776741 -250000 -250000 40026741 -1224018 -1224018 38802723 48814915 1224018 1224018 47590897 0 47590897 DESCRIPTION OF INTENDED USE OF ENDOWMENT FUNDS: PART V, LINE 4: THESE ENDOWMENT FUNDS ARE PLEDGED AS COLLATERAL FOR THE ORGANIZATION'S LONG-TERM DEBT. EARNINGS ON THE ENDOWMENT FUNDS ARE USED TO PARTIALLY FUND PAYMENT OF PRINCIPAL & INTEREST DUE ON THE DEBT. PART XI, LINE 8 - OTHER ADJUSTMENTS: ALLOWANCE FOR UNCOLLECTIBLE SECURITY DEPOSITS -250,000. PART XII, LINE 2D - OTHER ADJUSTMENTS: ALLOWANCE FOR UNCOLLECTIBLE SECURITY DEPOSITS -250,000. PART XII, LINE 4B - OTHER ADJUSTMENTS: RENTAL EXPENSES NETTED AGAINST REVENUES ON PART VIII -1,409,890. TENANT REVENUE NETTED WITH EXPENSES ON FINANCIAL STATEMENTS 185,872. PART XIII, LINE 2D - OTHER ADJUSTMENTS: RENTAL EXPENSES NETTED AGAINST REVENUES ON PART VIII 1,409,890. TENANT REVENUE NETTED WITH EXPENSES ON FINANCIAL STATEMENTS -185,872. X X X X X 1 0 0 0 0 0 0 0 0 LEROY HOOD MD PHD 375000 0 0 0 7509 0 24500 0 7462 0 414471 0 0 0 JAMES R LADD 280000 0 0 0 2420 0 24500 0 13315 0 320235 0 0 0 DAVID GALAS PHD 295000 0 0 0 3667 0 24500 0 7579 0 330746 0 0 0 JOHN AITCHISON PHD 174463 0 0 0 6053 0 17147 0 6377 0 204040 0 0 0 JOSEPH H NADEAU PHD 295000 0 0 0 2194 0 12250 0 13351 0 322795 0 0 0 CATHRYN CAMPBELL JD PHD 270000 0 0 0 2688 0 24500 0 7535 0 304723 0 0 0 ILYA SHMULEVICH PHD 197941 0 0 0 1422 0 20129 0 18848 0 238340 0 0 0 DIANE R ISONAKA 119436 0 0 0 89795 0 11566 0 9329 0 230126 0 0 0 NITIN S BALIGA PHD 201465 0 0 0 1491 0 10696 0 18629 0 232281 0 0 0 ALAN ADEREM PHD 118754 0 0 0 -2464 0 11262 0 6421 0 133973 0 0 0 PART I, LINE 4A DIANE ISONAKA'S SEVERANCE AGREEMENT WAS EFFECTIVE SEVEN DAYS AFTER THE DATE ON WHICH SHE SIGNED IT (SIGNED JULY 11, 2011; EFFECTIVE JULY 18, 2011). HER SEVERANCE PAY WAS NINE MONTHS OF HER REGULAR PAY AT TERMINATION ($16,222.50 PER MONTH). THE SEVERANCE PAYMENTS WERE MADE THROUGH ISB'S REGULAR PAYROLL AND SPREAD OVER 18 SEMI-MONTHLY PAY PERIODS BEGINNING IN THE PAY PERIOD ENDING JULY 31, 2011. ISB ALSO PAID SIX MONTHS OF COBRA MEDICAL INSURANCE PREMIUMS. JOHN AITCHISON RELOCATION ASSISTANCE X 75000 30000 0 0 1 INTEGRATED DIAGNOSTICS INC 2009 OPERATING EXPENSES (THRU 8/31/09) X 383550 335641 0 1 1 365641 FORM 990, PART I, LINE 6 THIRTEEN VOLUNTEERS SERVED AS INDIVIDUAL DIRECTORS ON ISB'S BOARD OF DIRECTORS DURING 2011. FORM 990, PART VI, SECTION A, LINE 2 LEIGHTON READ AND LOUIS LANGE HAVE A BUSINESS RELATIONSHIP. LEROY HOOD AND JAMES LADD HAVE A BUSINESS RELATIONSHIP. LEROY HOOD AND DAVID GALAS HAVE A BUSINESS RELATIONSHIP. MARK ASHIDA AND STEPHEN GRAHAM HAVE A BUSINESS RELATIONSHIP. FORM 990, PART VI, SECTION B, LINE 11 FORM 990 IS PREPARED WITH ASSISTANCE FROM A PAID PROFESSIONAL ADVISOR BASED ON INFORMATION PREPARED BY STAFF. THE DRAFT RETURN IS REVIEWED IN TURN BY THE DIRECTOR OF FINANCE, THE SENIOR VICE PRESIDENT FOR FINANCE & OPERATIONS, AND THEN BY THE AUDIT COMMITTEE OF THE BOARD OF DIRECTORS. THE FILING VERSION OF THE RETURN IS DISTRIBUTED ELECTRONICALLY TO ALL BOARD MEMBERS PRIOR TO FILING WITH THE IRS. FORM 990, PART VI, SECTION B, LINE 12C THE CONFLICT OF INTEREST (COI) POLICY APPLIES TO 'COVERED PERSONS', DEFINED AS ANY INSTITUTE (BOARD) DIRECTOR, OFFICER, OR ANY MEMBER OF ANY COMMITTEE OF THE INSTITUTE'S BOARD OF DIRECTORS THAT HAS AUTHORITY TO ACT ON BEHALF OF THE BOARD OF DIRECTORS. EACH COVERED PERSON SHALL PROMPTLY AND FULLY DISCLOSE ALL MATERIAL FACTS OF EVERY ACTUAL OR POTENTIAL CONFLICT OF INTEREST: [A] EXISTING AT THE TIME WHEN HE/SHE BECOMES A COVERED PERSON; [B] THAT ARISES WHILE HE/SHE IS A COVERED PERSON, AT THE TIME SUCH ACTUAL OR POTENTIAL CONFLICT ARISES; AND [C] THROUGH THE ANNUAL CIRCULATION OF THE FIDUCIARY COI QUESTIONNAIRE. THE VICE PRESIDENT OF FINANCE & ADMINSTRATION SHALL DISCLOSE TO THE BOARD OF DIRECTORS ALL CONFLICTS OF INTEREST REPORTED TO HIM OR HER UNDER THIS POLICY. THE BOARD OF DIRECTORS WILL EVALUATE THE DISCLOSURES TO DETERMINE WHETHER THEY INVOLVE ACTUAL CONFLICTS OF INTEREST AND MAY ATTEMPT TO DEVELOP ALTERNATIVES TO REMOVE THE CONFLICT FROM THE SITUATION. FORM 990, PART VI, SECTION B, LINE 15 DURING 2011, THE COMPENSATION OF THE INSTITUTE'S PRESIDENT WAS REVIEWED BY A PAID CONSULTANT TO DETERMINE ITS COMPARABILITY TO PREVAILING MARKET CONDITIONS FOR SIMILAR POSITIONS AT OTHER ORGANIZATIONS. THIS STUDY WAS PRESENTED TO AND APPROVED BY THE INSTITUTE'S GOVERNING BOARD OF DIRECTORS. ALSO, THE EMPLOYMENT AGREEMENT FOR THE INSTITUTE'S PRESIDENT WAS REVIEWED AND APPROVED BY THE INSTITUTE'S GOVERNING BOARD OF DIRECTORS. THE COMPENSATION OF ALL OTHER OFFICERS AND KEY EMPLOYEES ARE BASED UPON AND SUBJECT TO APPROVAL OF THE PRESIDENT. FORM 990, PART VI, SECTION C, LINE 19 THE INSTITUTE'S GOVERNING DOCUMENTS, CONFLICT OF INTEREST POLICY, AND FINANCIAL STATEMENTS ARE NOT MADE READILY AVAILABLE TO THE PUBLIC. THE INSTITUTE'S APPLICATION FOR TAX EXEMPT STATUS AND ITS ANNUAL FORM 990 ARE AVAILABLE FOR PUBLIC INSPECTION AND REVIEW UPON REQUEST. FORM 990, PART IX, LINE 24 THERE IS $2,887 OF UNRELATED BUSINESS INCOME TAX INCLUDED IN THE AMOUNT LISTED ON THIS LINE. CHANGES IN NET ASSETS OR FUND BALANCES: FORM 990, PART XI, LINE 5: ALLOWANCE FOR UNCOLLECTIBLE SECURITY DEPOSITS -250,000. TOTAL TO FORM 990, PART XI, LINE 5: -250,000.