Document:

exv10w54

 

Exhibit 10.54

INDEPENDENT CONTRACTOR SERVICES AGREEMENT

This Agreement is made as of July 28, 2006, (“Effective Date”) by and between Solexa,
Inc. and its successors or assignees (“Company”) and the undersigned Joseph E. Whitters
(“Contractor”).

1.1. Engagement of Services. Company may from time to time submit a Statement of
Work (“SOW”) to Contractor substantially in the form of Exhibit A to this Agreement. Subject to the
terms of this Agreement, Contractor will provide the services set forth in each SOW accepted by
Contractor (the “Project(s)”) by the completion dates set forth therein. The manner and means that
Contractor chooses to complete the Projects are in Contractor’s sole discretion and control.
Contractor shall perform the services necessary to complete the Projects in a timely and
professional manner consistent with industry standards and at a location, place and time that
Contractor deems appropriate. In completing the Projects, Contractor agrees to provide its own
equipment, tools, and other materials at its own expense; however, Company will make its facilities
and equipment available to Contractor when necessary.

2. Compensation.

     2.1 Fees. Company will pay Contractor the fee specified in each SOW as Contractor’s sole
compensation for the Project, provided such Project meets the terms of the SOW and this Agreement
and is of a quality consistent with industry standards. Contractor shall be responsible for all
expenses incurred in performing services under this Agreement, except as set forth in the SOW. Upon
termination of this Agreement for any reason prior to completion of an SOW, Company will pay
Contractor fees and expenses on the basis stated in the SOW for work which is then in progress,
within thirty (30) days of the later of Contractor’s invoice and the effective date of such
termination.

     2.2 Invoicing. Unless otherwise provided in the applicable SOW, (a) payment to Contractor of
undisputed fees will be due thirty (30) days following Company’s receipt of an invoice which
contains accurate records of the work performed sufficient to document the invoiced fees; and (b)
Contractor will submit invoices to Company upon completion of the milestones specified in the
applicable SOW or, if no such milestones are specified, on a monthly basis for services performed
in the previous month.

3. Independent Contractor Relationship. Contractor’s relationship with Company will be
that of an independent contractor, and nothing in this Agreement should be construed to create a
partnership, joint venture, or employer-employee relationship. Contractor (a) is not the agent of
Company; (b) is not authorized to make any representation, contract, or commitment on behalf of
Company; (c) will not be entitled to any of the benefits that Company makes available to its
employees, such as group insurance, profit-sharing or retirement benefits (and waives the right to
receive any such benefits); and (d) will be solely responsible for all tax returns and payments
required to be filed with or made to any federal, state, or local tax authority with respect to
Contractor’s performance of services and receipt of fees under this Agreement. If applicable,
Company will report amounts paid to Contractor by filing Form 1099-MISC with the Internal Revenue
Service, as required by law. Contractor agrees to accept exclusive liability for complying with all
applicable state and federal laws, including laws governing self-employed individuals, if
applicable, such as laws related to payment of taxes, social security, disability, and other
contributions based on fees paid to Contractor under this Agreement. Company will not withhold or
make payments for social security, unemployment insurance or disability insurance contributions, or
obtain workers’ compensation insurance on Contractor’s behalf. Contractor hereby agrees to
indemnify and defend Company against any and all such taxes or contributions, including penalties
and interest. Contractor agrees to provide proof of payment of appropriate taxes on any fees paid
to Contractor under this Agreement upon reasonable request of Company.

4. Intellectual Property Rights.

     4.1 Confidential Information. Contractor agrees that during the term of this Agreement and
thereafter, except as expressly authorized in writing by the Chief Executive Officer (the “CEO”) of
Company, it (a) will not use or permit the use of Confidential Information (defined below) in any
manner or for any purpose not expressly set forth in this Agreement; (b) will not disclose, lecture
upon, publish, or permit others to disclose, lecture upon, or publish any such Confidential
Information to any third party without first obtaining the CEO’s express written consent on a
case-by-case basis; (c) will limit access to Confidential Information to Contractor personnel who
need to know such information in connection with their work for Company; and (d) will not remove
any tangible embodiment of any Confidential Information from Company’s premises without Company’s
prior written consent. “Confidential Information” includes, but is not limited to, all information
related to Company’s business and its actual or anticipated research and development, including
without limitation (i) trade secrets, inventions, ideas, processes, computer source and object
code, formulae, data, programs, other works of authorship, know-how, improvements, discoveries,
developments, designs, and techniques; (ii) information regarding products or plans for research
and development, marketing and business plans, budgets, financial statements, contracts, prices,
suppliers, and customers; (iii) information regarding the skills and compensation of Company’s
employees, contractors, and any other service providers of Company; (iv) the existence of any
business discussions, negotiations, or agreements between Company and any third party; and (v) all
such information related to any third party that is disclosed to Company or to Contractor during
the course of Company’s business (“Third

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Party Information”). Notwithstanding the foregoing, it is understood that Contractor is free
to use information which is generally known in the trade or industry, information which is not
gained as a result of a breach of this Agreement, and Contractor’s own skill, knowledge, know-how,
and experience.

     4.2 Competitive or Conflicting Engagements. Contractor agrees, during the term of this
Agreement, not to enter into a contract or accept an obligation that is inconsistent or
incompatible with Contractor’s obligations under this Agreement. Contractor warrants that there is
no such contract or obligation in effect as of the Effective Date. Contractor further agrees not to
disclose to Company, bring onto Company’s premises, or induce Company to use any confidential
information that belongs to anyone other than Company or Contractor. In addition, Contractor agrees
that, during the term of this Agreement, it will not perform, or agree to perform, any services for
any third party that engages, or plans to engage, in any business or activity competitive with that
of Company.

     4.3 Inventions and Intellectual Property Rights. As used in this Agreement, the term
“Invention” means any ideas, concepts, information, materials, processes, data, programs, know-how,
improvements, discoveries, developments, designs, artwork, formulae, other copyrightable works, and
techniques and all Intellectual Property Rights therein. The term “Intellectual Property Rights”
means all trade secrets, copyrights, trademarks, mask work rights, patents and other intellectual
property rights recognized by the laws of any country.

     4.4 Background Technology. As used in this Agreement, the term “Background Technology” means
all Inventions developed by Contractor other than in the course of providing services to Company
hereunder and all Inventions acquired or licensed by Contractor that Contractor uses in performing
services under this Agreement or incorporates into Work Product (defined below). Contractor will
disclose any Background Technology in the SOW in which Contractor proposes to use or incorporate
such Background Technology. If no Background Technology is disclosed in an SOW, Contractor
warrants that it will not use Background Technology or incorporate it into Work Product provided
pursuant thereto. Notwithstanding the foregoing, Contractor agrees that it will not incorporate
into Work Product or otherwise deliver to Company any software code licensed under the GNU GPL or
LGPL or any other license that by its terms requires, or conditions the use or distribution of such
code on, the disclosure, licensing, or distribution of the Work Product or any source code owned or
licensed by the Company.

     4.5 License to Background Technology. Contractor hereby grants to Company a non-exclusive,
perpetual, fully-paid and royalty-free, irrevocable and world-wide right, with rights to sublicense
through multiple levels of sublicensees, to reproduce, make derivative works of, distribute,
publicly perform, and publicly display in any form or medium, whether now known or later developed,
make, have made, use, sell, import, offer for sale, and exercise any and all present or future
rights in the Background Technology incorporated or used in Work Product for the purpose of
developing and marketing Company products.

     4.6 Disclosure of Work Product. As used in this Agreement, the term “Work Product” means any
Invention that is solely or jointly conceived, made, reduced to practice, or learned by Contractor
in the course of any services performed for Company or with the use of materials of Company during
the term of this Agreement. Contractor agrees to disclose promptly in writing to Company, or any
person designated by Company, all Work Product.

     4.7 Ownership of Work Product. Contractor agrees that any and all Work Product shall be the
sole and exclusive property of Company.

     4.8 Assignment of Work Product. If Contractor has any rights to the Work Product that are not
owned by Company upon creation or embodiment, Contractor irrevocably assigns to Company all right,
title and interest worldwide in and to such Work Product. Except as set forth below, Contractor
retains no rights to use the Work Product and agrees not to challenge the validity of Company’s
ownership in the Work Product.

     4.9 Waiver or Assignment of Other Rights. If Contractor has any rights to the Work Product
that cannot be assigned to Company, Contractor unconditionally and irrevocably waives the
enforcement of such rights, and all claims and causes of action of any kind against Company with
respect to such rights, and agrees, at Company’s request and expense, to consent to and join in any
action to enforce such rights. If Contractor has any right to the Work Product that cannot be
assigned to Company or waived by Contractor, Contractor unconditionally and irrevocably grants to
Company during the term of such rights, an exclusive, irrevocable, perpetual, worldwide, fully paid
and royalty-free license, with rights to sublicense through multiple levels of sublicensees, to
reproduce, make derivative works of, distribute, publicly perform and publicly display in any form
or medium, whether now known or later developed, make, use, sell, import, offer for sale and
exercise any and all such rights.

     4.10 Assistance. Contractor agrees to assist Company in every way, both during and after the
term of this Agreement, to obtain and enforce United States and foreign Intellectual Property
Rights relating to Work Product in all countries. In the event Company is unable to secure
Contractor’s signature on any document needed in connection with such purposes, Contractor hereby
irrevocably designates and appoints Company and its duly authorized officers and agents as its
agent and attorney in fact, which appointment is coupled with an interest, to act on its behalf to
execute and file any such documents and to do all other lawfully permitted acts

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to further such purposes with the same legal force and effect as if executed by Contractor.

5. Contractor Representations and Warranties. Contractor hereby represents and warrants
that (a) the Work Product will be an original work of Contractor and any third parties will have
executed assignment of rights reasonably acceptable to Company prior to being allowed to
participate in the development of the Work Product; (b) the Work Product will fully conform to the
requirements and terms set forth in the SOW; (c) neither the Work Product nor any element thereof
will infringe or misappropriate the Intellectual Property Rights of any third party; (d) neither
the Work Product nor any element thereof will be subject to any restrictions or to any mortgages,
liens, pledges, security interests, or encumbrances; (e) Contractor will not grant, directly or
indirectly, any rights or interest whatsoever in the Work Product to third parties; (f) Contractor
has full right and power to enter into and perform this Agreement without the consent of any third
party; (g) Contractor has an unqualified right to grant the license to all Background Technology as
set forth in the section titled “License to Background Technology” to Company; (h) Contractor will
comply with all laws and regulations applicable to Contractor’s obligations under this Agreement;
and (i) should Company permit Contractor to use any of Company’s equipment, or facilities during
the term of this Agreement, such permission shall be gratuitous and Contractor shall be responsible
for any injury to any person (including death) or damage to property arising out of use of such
equipment or facilities.

6. Indemnification. Contractor will indemnify and hold harmless Company, its officers,
directors, employees, sublicensees, customers and agents from any and all claims, losses,
liabilities, damages, expenses and costs (including attorneys’ fees and court costs) which result
from a breach or alleged breach of any representation or warranty of Contractor (a “Claim”) in this
Agreement or any intentional misconduct or negligence by Contractor or any of its subcontractors,
employees, or agents in performing services under this Agreement. From the date of written notice
from Company to Contractor of any such Claim, Company shall have the right to withhold from any
payments due Contractor under this Agreement the amount of any defense costs, plus additional
reasonable amounts as security for Contractor’s obligations under this section.

7. Termination.

     7.1 Termination without Cause. Company may terminate this Agreement without cause at its
convenience upon fifteen (15) days’ prior written notice to Contractor. Contractor may terminate
this Agreement at any time that there is no uncompleted SOW in effect upon fifteen (15) days’ prior
written notice to Company. Company will pay Contractor only those fees and expenses related to
services actually performed during such notice period, as specified in the SOW.

     7.2 Termination with Cause. Either party may terminate this Agreement immediately in the
event that the other party has materially breached the Agreement and fails to cure such breach
within fifteen (15) days of receipt of notice by the non-breaching party, setting forth in
reasonable detail the nature of the breach. Company may also terminate this Agreement immediately
in its sole discretion in the event of Contractor’s material breach of the section titled
“Intellectual Property Rights.” Company will pay Contractor only those fees and expenses related
to services actually performed during such notice period, as specified in the SOW.

     7.3 Return of Company Property. Upon termination of the Agreement or upon Company’s request at
any other time, Contractor will deliver to Company all of Company’s property, equipment, and
documents, together with all copies thereof, and any other material containing or disclosing any
Work Product, Third Party Information or Confidential Information of Company and certify to Company
in writing that Contractor has fully complied with this obligation Contractor further agrees that
any property situated on Company’s premises and owned by Company is subject to inspection by
Company personnel at any time with or without notice.

     7.4 Survival. The following provisions shall survive termination of this Agreement: Sections
titled “Intellectual Property Rights,” “Contractor Representations and Warranties,”
“Indemnification,” “Return of Company Property,” “Survival,” and “General Provisions.”

8. Multi-Employee Contractor. If Contractor will be hiring employees or agents to provide
services pursuant to this Agreement, Contractor must obtain Company’s prior written consent to such
hiring, and before any Contractor employee or agent performs services in connection with this
Agreement or has access to Confidential Information, the employee or agent and Contractor must have
entered into a binding written agreement expressly for the benefit of Company that contains
provisions substantially equivalent to the sections of this Agreement titled “Engagement of
Services” and “Intellectual Property Rights.” At Company’s request, Contractor will provide
Company with copies of such agreements. Company reserves the right to refuse or limit Contractor’s
use of any employee or agent or to require Contractor to remove any employee or agent already
engaged in the performance of the services. Company’s exercise of such right will in no way limit
Contractor’s obligations under this Agreement. Contractor agrees (a) that its employees and agents
shall not be entitled to or eligible for any benefits that Company may make available to its
employees; (b) to limit access to the Confidential Information to employees or agents of Contractor
who have a reasonable need to have such access in order to perform the services pursuant to this
Agreement; and (c) to be solely responsible for all expenses incurred by any of its employees or
agents in performing the services or otherwise performing its obligations under this Agreement,
except as set forth in the SOW.

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9. General Provisions.

     8.1 Governing Law and Venue. This Agreement and any action related thereto will be governed,
controlled, interpreted, and defined by and under the laws of the State of California, without
giving effect to any conflicts of laws principles that require the application of the law of a
different state. Contractor hereby expressly consents to the personal jurisdiction and venue in
the state and federal courts for the county in which Company’s principal place of business is
located for any lawsuit filed there against Contractor by Company arising from or related to this
Agreement.

     9.2 Severability. If any provision of this Agreement is, for any reason, held to be invalid or
unenforceable, the other provisions of this Agreement will be unimpaired and the invalid or
unenforceable provision will be deemed modified so that it is valid and enforceable to the maximum
extent permitted by law.

     9.3 No Assignment. This Agreement, and Contractor’s rights and obligations herein, may not be
assigned, subcontracted, delegated, or otherwise transferred by Contractor without Company’s prior
written consent, and any attempted assignment, subcontract, delegation, or transfer in violation of
the foregoing will be null and void. The terms of this Agreement shall be binding upon assignees.

     9.4 Notices. Each party must deliver all notices or other communications required or permitted
under this Agreement in writing to the other party at the address listed on the signature page, by
courier, by certified or registered mail (postage prepaid and return receipt requested), or by a
nationally-recognized express mail service. Notice will be effective upon receipt or refusal of
delivery. If delivered by certified or registered mail, any such notice will be considered to have
been given five (5) business days after it was mailed, as evidenced by the postmark. If delivered
by courier or express mail service, any such notice shall be considered to have been given on the
delivery date reflected by the courier or express mail service receipt. Each party may change its
address for receipt of notice by giving notice of such change to the other party.

     9.5 Injunctive Relief. Contractor acknowledges that, because its services are personal and
unique and because Contractor will have access to Confidential Information of Company, any breach
of this Agreement by Contractor would cause irreparable injury to Company for which monetary
damages would not be an adequate remedy and, therefore, will entitle Company to injunctive relief
(including specific performance). The rights and remedies provided to each party in this Agreement
are cumulative and in addition to any other rights and remedies available to such party at law or
in equity.

     9.6 Waiver. Any waiver or failure to enforce any provision of this Agreement on one occasion
will not be deemed a waiver of any other provision or of such provision on any other occasion.

     9.7 Export. Contractor agrees not to export, directly or indirectly, any U.S. technical data
acquired from Company or any products utilizing such data, to countries outside the United States,
because such export could be in violation of the United States export laws or regulations.

     9.8 Entire Agreement. This Agreement, together with the Nondisclosure Agreement dated as of
May 16, 2006, is the final, complete and exclusive agreement of the parties with respect to the
subject matters hereof and supersedes and merges all prior discussions between the parties with
respect to such subject matters. No modification of or amendment to this Agreement, or any waiver
of any rights under this Agreement, will be effective unless in writing and signed by Contractor
and CEO of the Company. The terms of this Agreement will govern all SOWs and services undertaken by
Contractor for Company. In the event of any conflict between this Agreement and a SOW, the terms of
the SOW shall govern, but only with respect to the services set forth therein.

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In Witness Whereof, the parties have caused this Independent Contractor Services Agreement
to be executed by their duly authorized representatives.

	 	 	 	 	 	 	 	 	 
	Company:	 	 	 	Contractor:
	/s/
John West 
	 	 	 	/s/ Joseph E. Whitters 	 	 
	 	 	 	 	 
	(Signature)	 	 	 	(Signature)
	 
	 	 	 	 	 	 	 	 
	By: John West

	 	 	 	By:	 	/s/ Joseph E. Whitters 
	 	 	 	 	 	 	 
	Title: CEO
Address: 25861 Industrial Blvd. / Hayward, CA 94545

	 	 	 	Title:	 	 
	 
		 	 	 	Address:	 	 	 	 
	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	 	 	 	 	If Contractor is a natural person, Contractor must provide the
following information for copyright registration purposes only:
	 
	 	 	 	 	Date of Birth:	 	 
	 

	 	 	 	 	 	 	 	 
	 
	 	 	 	 	Nationality or Domicile:	 	 
	 

	 	 	 	 	 	 	 	 

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EXHIBIT A

Statement of Work

This Statement of Work (“SOW”) is incorporated into the Independent Contractor Services Agreement
by and between Company and Contractor. This SOW describes services and Work Product to be
performed and provided by Contractor pursuant to the Agreement. If any item in this SOW is
inconsistent with the Agreement prior to such incorporation, the terms of this SOW will control,
but only with respect to the services to be performed under this SOW.

1. Scope of Services:

     a. Participating in the activities of and advising Company’s Audit Committee of the Board of
Directors, although not as a member of this committee.

     b. Other financial consulting projects as agreed with Company executive management.

     This Agreement does not cover matters related to Contractor’s activities as a member of
Company’s Board of Directors of committees of the Board of Directors, for which Contractor will be
compensated as a Company director.

2. Payment of Fees. Fee will be payable in Company common stock; management will recommend to the
Compensation Committee of the Company’s Board of Directors that Contractor be issued a grant of
7,500 shares of unvested restricted stock to be vested based on fees earned as described below.

For participation in the activities of and advising Company’s Audit Committee of the Board of Directors:

	 	•	 	Monthly retainer fee of $625.00; plus
	 
	 	•	 	Per meeting fees of:

	 	o	 	$1,000.00 for in-person meetings on the same day as a board meeting
	 
	 	o	 	$2,000.00 for other in-person meetings
	 
	 	o	 	$500.00 for telephonic meetings on the same day as a board meeting
	 
	 	o	 	$1,000.00 for other telephonic meetings

For other financial consulting projects: Time and materials at a rate: $312.50 per hour, up to the
greater of time spent on working on Company matters or a maximum of $2,500.00 per travel day if
travel is in excess of eight hours. Fee invoiced by Contractor at the rates set forth below.

In no event will Company compensate Contractor under this consulting contract in an amount greater
than $60,000.00 (sixty thousand dollars) in any twelve month period while Consultant is a member
of Company’s board of directors. Compensation refers to the market value of restricted stock on
the date of vesting plus any cash payments.

 

3. Expenses. Company will reimburse Contractor for the following expenses: traveling to Solexa
arranged meetings, phone and other incidental expenses related to consulting activities

      

4. Duration: Cancellable at 30 days notice by either party, or immediately if Contractor joins the
Audit Committee of the Company’s Board of Directors.

          Background Technology Disclosure. None

	 	 	 	 	 	 	 	 	 	 	 
	 	 	 
	 
	Signed:
	 	/s/ John West 	 	 	 	/s/ Joseph E. Whitters 	 	 
	 

	 	 

Chief Executive Officer, Solexa, Inc.
	 	 
	 	Contractor
	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	Dated:

	 	August 2, 2006 	 	 	 	Dated:	 	8/2/06exv10w55

 

Exhibit 10.55

INDEMNITY AGREEMENT

     THIS AGREEMENT is made and entered into as of the 28th day of July, 2006 by and between
SOLEXA, INC., a Delaware corporation (the “Corporation”), and JOSEPH WHITTERS (the “Agent”).

RECITALS

     WHEREAS, Agent will perform a valuable service to the Corporation in his capacity as a
DIRECTOR of Board of Directors of the Corporation;

     WHEREAS, the stockholders of the Corporation have adopted bylaws (the “Bylaws”) providing for
the indemnification of the directors, officers, employees and other agents of the Corporation,
including persons serving at the request of the Corporation in such capacities with other
corporations or enterprises, as authorized by the Delaware General Corporation Law, as amended (the
“Code”); and

     WHEREAS, the Bylaws and the Code, by their non-exclusive nature, permit contracts between the
Corporation and its agents, officers, employees and other agents with respect to indemnification of
such persons;

     NOW, THEREFORE, in consideration of Agent’s service as a Director of the Corporation after the
date hereof, the parties hereto agree as follows:

AGREEMENT

     1. Services to the Corporation. Agent will serve, at the will of the Corporation or under
separate contract, if any such contract exists, as Director of the Corporation; provided, however,
that Agent may at any time and for any reason resign from such position or any other position
(subject to any contractual obligation that Agent may have assumed apart from this Agreement) and
that the Corporation shall have no obligation under this Agreement to continue Agent in such
position or any other position.

     2. Indemnity of Agent. The Corporation hereby agrees to hold harmless and indemnify Agent to
the fullest extent authorized or permitted by the provisions of the Bylaws and the Code, as the
same may be amended from time to time (but, only to the extent that such amendment permits the
Corporation to provide broader indemnification rights than the Bylaws or the Code permitted prior
to adoption of such amendment).

     3. Additional Indemnity. In addition to and not in limitation of the indemnification otherwise
provided for herein, and subject only to the exclusions set forth in Section 4 hereof, the
Corporation hereby further agrees to hold harmless and indemnify Agent:

          (a) from and against any and all Expenses (as defined below) paid or payable by Agent in
connection with or in respect of a Claim (as defined below). “Claim” means any threatened, pending
or completed action, suit, proceeding or alternative dispute resolution mechanism, or any inquiry,
hearing or investigation, whether instituted by the Corporation or any other party, that Agent in
good faith believes might lead to the institution of any such action, suit, proceeding or
alternative dispute resolution whether civil, criminal, administrative, investigative or otherwise,
each of the foregoing by reason of the fact that Agent is, was or at any time becomes a director,
officer, employee or other agent of Corporation, or is or was serving or at any time serves at the
written request of the Corporation as a director, officer, employee or other agent of another
corporation, partnership, joint venture, trust, employee benefit plan or other enterprise.
“Expense” means any and all expenses (including attorneys’ fees), witness fees,

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damages, judgments,
fines and amounts paid in settlement and any other amounts paid or incurred by Agent in connection
with investigating, defending, being a witness in or participating in (including on
appeal), or preparing to defend, be a witness in or participate in any Claim; any and all
judgments, fines, losses, liabilities, penalties, and amounts paid in settlement of any such claim;
and

          (b) otherwise to the fullest extent as may be provided to Agent by the Corporation under the
non-exclusivity provisions of the Code and Section 42 of the Bylaws.

     4. Limitations on Additional Indemnity.

          (a) No indemnity pursuant to Section 3 hereof shall be paid by the Corporation:

               (i) on account of any claim against Agent for an accounting of profits made from the purchase
or sale by Agent of securities of the Corporation pursuant to the provisions of Section 16(b) of
the Securities Exchange Act of 1934 and amendments thereto (the “Exchange Act”) or similar
provisions of any federal, state or local statutory law;

               (ii) on account of Agent’s conduct that was knowingly fraudulent or deliberately dishonest or
that constituted willful misconduct;

               (iii) on account of Agent’s conduct that constituted a breach of Agent’s duty of loyalty to
the Corporation or resulted in any personal profit or advantage to which Agent was not legally
entitled;

               (iv) for which payment actually has been made to Agent under a valid and collectible insurance
policy or under a valid and enforceable indemnity clause, bylaw or agreement, except in respect of
any excess beyond payment under such insurance, clause, bylaw or agreement;

               (v) if indemnification is not lawful (and, in this respect, both the Corporation and Agent
have been advised that the Securities and Exchange Commission believes that indemnification for
liabilities arising under the federal securities laws is against public policy and is, therefore,
unenforceable and that claims for indemnification should be submitted to appropriate courts for
adjudication); or

               (vi) in connection with any proceeding (or part thereof) initiated by Agent, or any proceeding
by Agent against the Corporation or its directors, officers, employees or other agents, unless (i)
such indemnification is expressly required to be made by law, (ii) the proceeding was authorized by
the Board of Directors of the Corporation, (iii) such indemnification is provided by the
Corporation, in its sole discretion, pursuant to the powers vested in the Corporation under the
Code, or (iv) the proceeding is initiated pursuant to Section 9 hereof.

          (b) Within thirty (30) days of receipt of a notice pursuant to Section 7, the Corporation (or
the Independent Legal Counsel, if applicable) shall make an initial good faith determination of
Agent’s entitlement to indemnification pursuant to this Agreement and shall notify Agent (and the
Corporation, if Independent Legal Counsel is making such determination) promptly of such
determination. If at any time thereafter the Corporation (or the Independent Legal Counsel, as
applicable) in good faith determines that any indemnification requested pursuant to this Agreement
is prohibited pursuant to Section 4(a), the Corporation shall promptly provide notice of such
determination to Agent (and the Corporation, if applicable). Any determination by the Corporation
pursuant to this Section 4(b) shall be made by the Corporation’s Board of Directors.

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     5. Continuation of Indemnity. All agreements and obligations of the Corporation contained
herein shall continue during the period Agent is a director, officer, employee or other agent of
the Corporation (or is or was serving at the written request of the Corporation as a director,
officer, employee or other agent of another corporation, partnership, joint venture, trust,
employee benefit plan or other enterprise) and shall continue thereafter so long as Agent shall be
subject to any possible Claim.

     6. Partial Indemnification. Agent shall be entitled under this Agreement to indemnification by
the Corporation for a portion of the Expenses that Agent pays or incurs in connection with Claim
even if Agent is not entitled hereunder to indemnification for the total amount thereof, and the
Corporation shall indemnify Agent for the portion thereof to which Agent is entitled.

     7. Notification and Defense of Claim. Not later than thirty (30) days after receipt by Agent
of notice of any Claim, Agent will, if a claim in respect thereof is to be made against the
Corporation under this Agreement, notify the Corporation of the commencement of such Claim;
provided, however, that no failure to provide such notice shall be deemed to reduce or limit the
obligations of the Corporation under this Agreement unless (and only to the extent that) such
failure materially prejudices the Corporation. The omission so to notify the Corporation will not
relieve it from any liability which it may have to Agent otherwise than under this Agreement. With
respect to any Claim as to which Agent notifies the Corporation of the commencement thereof:

          (a) The Corporation will be entitled to participate therein at its own expense;

          (b) Except as otherwise provided below, the Corporation may, at its option and jointly with
any other indemnifying party similarly notified and electing to assume such defense, assume the
defense thereof, with counsel reasonably satisfactory to Agent. After notice from the Corporation
to Agent of its election to assume the defense thereof, the Corporation will not be liable to Agent
under this Agreement for any legal fees and expenses subsequently incurred by Agent in connection
with the defense thereof except for reasonable costs of investigation or otherwise as provided
below. Agent shall have the right to employ separate counsel in such action, suit or proceeding but
the fees and expenses of such counsel incurred after notice from the Corporation of its assumption
of the defense thereof shall be at the expense of Agent unless (i) the employment of counsel by
Agent has been authorized by the Corporation, (ii) Agent shall have reasonably concluded that there
may be a conflict of interest between the Corporation and Agent in the conduct of the defense of
such action (which conclusion may be made at any time during the pendency of the proceeding) or
(iii) the Corporation shall not in fact have employed or continue to employ counsel to assume the
defense of such action, in each of which cases the fees and expenses of Agent’s separate counsel
shall be at the expense of the Corporation. The Corporation shall not be entitled to assume the
defense of any Claim brought by or on behalf of the Corporation (except for a shareholders’
derivative suit brought nominally in the name of the Corporation) or as to which Agent shall have
made the conclusion provided for in clause (ii) above;

          (c) The Corporation shall not be liable to indemnify Agent under this Agreement for any
amounts paid in settlement of any Claim effected without its written consent, which shall not be
unreasonably withheld. The Corporation shall be permitted to settle any Claim except that it shall
not settle any Claim without Agent’s prior written consent (which may be given or withheld in
Agent’s sole discretion) in any manner which (a) would impose any penalty or limitation on Agent or
(b) would admit any liability or, misconduct by Agent;

          (d) If there is a Change in Control (as defined below) of the Corporation, then with respect
to all matters thereafter arising concerning the rights of Agent to indemnity expense payments
and/or advances under this Agreement or any other agreement or Corporation Bylaw now or hereafter
in effect, the Corporation shall seek legal advice only from Independent Legal Counsel (defined
below)

Page 3 of 6

 

selected by Agent and approved by the Corporation (which approval shall not be unreasonably
withheld). Such counsel, among other things, shall render its written opinion to the Corporation
and Agent as to
whether and to what extent Agent would be permitted to be indemnified under applicable law. The
Corporation shall pay the reasonable fees of such Independent Legal Counsel and fully indemnify
such counsel against any and all expenses (including attorneys’ fees), claims, liabilities and
damages arising out of or relating to this Agreement or its engagement pursuant hereto;

          (e) For purposes of this Section, a “Change in Control” shall be deemed to have occurred if
(i) any “person” (as such term is used in Sections 13(d) and 14(d) of the Exchange Act), other than
a trustee or other fiduciary holding securities under an employee benefit plan of the Corporation
or a corporation owned directly or indirectly by the stockholders of the Corporation in
substantially the same proportions as their ownership of the stock of the Corporation, becomes the
“beneficial owner” (as defined in Rule 13d-3 under the Exchange Act), directly or indirectly, of
securities of the Corporation representing 20% or more of the total voting power represented by the
Corporation’s then outstanding voting securities, (ii) during any period of two consecutive years,
individuals who at the beginning of such period constitute the Board of Directors of the
Corporation and any new director whose election by the Board of Directors or nomination for
election by the Corporation’s stockholders was approved by a vote of at least two-thirds (2/3) of
the directors still in office who either were directors at the beginning of the period or whose
election or nomination for election was previously so approved, cease for any reason to constitute
a majority thereof, (iii) the stockholders of the Corporation approve a merger or consolidation of
the Corporation with any other corporation, other than a merger or consolidation that would result
in the voting securities of the Corporation outstanding immediately prior thereto continuing to
represent (either by remaining outstanding or by being converted into voting securities of the
surviving entity) at least 80% of the total voting power represented by the voting securities of
the Corporation or such surviving entity outstanding immediately after such merger or
consolidation, or (iv) the stockholders or the Corporation approve a plan of complete liquidation
of the Corporation or an agreement for the sale or disposition by the Company of (in one
transaction or a series of transactions) all or substantially all of the Corporation’s assets; and

          (f) For purposes of this Section, “Independent Legal Counsel” shall be defined as an attorney
or firm of attorneys, selected in accordance with this Section, who have not otherwise performed
services for the Corporation or Agent within the last five years (other than as Independent Legal
Counsel under this Agreement or of other agents of the Corporation under similar indemnity
agreements).

     8. Expenses. The Corporation shall advance, promptly following request therefore, all expenses
incurred by Agent in connection with a Claim (an “Expense Advancement”). Notwithstanding the
foregoing, (i) the obligations of Corporation under this Section 8 shall be subject to the
condition that the Corporation (or Independent Legal Counsel, if applicable) shall not have
determined in good faith (in a written opinion, in the case of Independent Legal Counsel) pursuant
to Section 4(b) that Agent would not be permitted to be indemnified under this Agreement, and (ii)
the obligation of the Corporation to make an Expense Advancement shall be subject to the condition
that if, when and to the extent that the Corporation (or Independent Legal Counsel, if applicable)
determines that Agent would not be permitted to be indemnified under this Agreement, the
Corporation shall be entitled to be reimbursed by Agent for all such amounts theretofore paid, and
(iii) the corporation shall have received an undertaking by or on behalf of Agent to repay said
amounts if it shall be determined ultimately that Agent is not entitled to be indemnified under the
provisions of this Agreement, the Bylaws, the Code or otherwise; provided, however, that if Agent
has commenced or thereafter commences a legal proceeding in a court of competent jurisdiction to
secure a determination that Agent should be indemnified under this Agreement, any determination
made by the Corporation (or Independent Legal Counsel, if applicable) that Agent should not be
indemnified under this Agreement shall not be binding, the Corporation shall pay the Expenses or
Expense Advancement for which Agent seeks payment in such legal proceeding (subject to

Page 4 of 6

 

potential
reimbursement by Agent) and Agent shall not be required to reimburse the Corporation for any
Expenses or Expense Advancement until a final judicial determination is made with respect thereto.
Agent’s obligation to reimburse the Corporation for any Expense Advancement shall be unsecured and
no interest shall be charged thereon.

     9. Enforcement. Any right to indemnification or advances granted by this Agreement to Agent
shall be enforceable by or on behalf of Agent in any court of competent jurisdiction if (i) the
claim for indemnification or advances is denied, in whole or in part, or (ii) no disposition of
such claim is made within ninety (90) days of request therefore. It shall be a defense to any
action for which a claim for indemnification is made under Section 3 hereof (other than an action
brought to enforce a claim for expenses pursuant to Section 8 hereof, provided that the required
undertaking has been tendered to the Corporation) that Agent is not entitled to indemnification
because of the limitations set forth in Section 4 hereof. Neither the failure of the Corporation
(including its Board of Directors or its stockholders) to have made a determination prior to the
commencement of such enforcement action that indemnification of Agent is proper in the
circumstances, nor an actual determination by the Corporation (including its Board of Directors or
its stockholders) that such indemnification is improper shall be a defense to the action or create
a presumption that Agent is not entitled to indemnification under this Agreement or otherwise. For
purposes of this Agreement, the termination of any Claim, by judgment, order, settlement (whether
with or without court approval) or conviction, or upon a plea of nolo contendere,
or its equivalent, shall not create a presumption that Agent did not meet any particular standard
of conduct or have any particular belief or that a court has determined that indemnification is not
permitted by applicable law.

     10. Subrogation. In the event of payment under this Agreement, the Corporation shall be
subrogated to the extent of such payment to all of the rights of recovery of Agent, who shall
execute all documents required and shall do all acts that may be necessary to secure such rights
and to enable the Corporation effectively to bring suit to enforce such rights.

     11. Indemnification for Additional Expenses. In the event that any action is instituted (i)
by Agent pursuant to Section 9; (ii) by the Corporation for recovery of any Expense Advancement by
the Corporation to Agent, or (iii) by or in the name of the Corporation under this Agreement to
enforce or interpret any of the terms of this Agreement, Agent shall be entitled to be paid all
expenses (including, without limitation, attorneys’ and expert witness’ fees and all other costs,
expenses and obligations paid or incurred in connection with such matter) incurred by Agent with
respect to such action and Agent shall be entitled to the advancement of expenses with respect to
such action. Agent hereby undertakes to repay such amounts advanced if, and to the extent that, it
shall ultimately be determined that Agent is not entitled to be indemnified by the Company as
authorized by this Agreement, consistent with the terms of Sections 6 and 8.

     12. Non-Exclusivity of Rights. The rights conferred on Agent by this Agreement shall not be
exclusive of any other right which Agent may have or hereafter acquire under any statute, provision
of the Corporation’s Certificate of Incorporation or Bylaws, agreement, vote of stockholders or
directors, or otherwise, both as to action in her official capacity and as to action in another
capacity while holding office. To the extent that a change in the applicable law (whether by
statute or judicial decision) permits greater indemnification by agreement than would be afforded
currently under any applicable Bylaws or this Agreement, it is the intent of the parties hereto
that Agent shall enjoy by this Agreement the greater benefits so afforded by such change.

13. Survival of Rights.

          (a) The rights conferred on Agent by this Agreement shall continue after Agent has ceased to
be a director, officer, employee or other agent of the

Page 5 of 6

 

Corporation or to serve at the request of
the Corporation as a director, officer, employee or other agent of another corporation,
partnership, joint venture, trust, employee benefit plan or other enterprise and shall inure to the
benefit of Agent’s heirs, executors and administrators.

          (b) The Corporation shall require any successor (whether direct or indirect, by purchase,
merger, consolidation or otherwise) to all or substantially all of the business or assets of the
Corporation, expressly to assume and agree to perform this Agreement in the same manner and to the
same extent that the Corporation would be required to perform if no such succession had taken
place.

     14. Separability. Each of the provisions of this Agreement is a separate and distinct
agreement and independent of the others, so that if any provision hereof shall be held to be
invalid for any reason, such invalidity or unenforceability shall not affect the validity or
enforceability of the other provisions hereof. Furthermore, if this Agreement shall be invalidated
in its entirety on any ground, then the Corporation shall nevertheless indemnify Agent to the
fullest extent provided by the Bylaws, the Code or any other applicable law.

     15. Governing Law. This Agreement shall be interpreted and enforced in accordance with the
laws of the State of Delaware.

     16. Amendment and Termination. No amendment, modification, termination or cancellation of this
Agreement shall be effective unless in writing signed by both parties hereto.

     17. Entire Agreement; Identical Counterparts. This Agreement constitutes the entire Agreement
and supersedes all prior agreements and understandings, both written and oral, between the parties
with respect to the subject matter hereof. This Agreement may be executed in one or more
counterparts, each of which shall for all purposes be deemed to be an original but all of which
together shall constitute but one and the same Agreement. Only a counterpart signed by Agent need
be produced to evidence the existence of this Agreement.

     18. Headings. The headings of the sections of this Agreement are inserted for convenience only
and shall not be deemed to constitute part of this Agreement or to affect the construction hereof.

     19. Notices. All notices, requests, demands and other communications hereunder shall be in
writing and shall be deemed to have been duly given (i) upon delivery if delivered by hand to the
party to whom such communication was directed; (ii) upon the third business day after the date on
which such communication was mailed if mailed by certified or registered mail with postage prepaid;
(ii) the following business day if sent by overnight delivery using a nationally recognized courier
service, such as Federal Express or UPS :

          (a) If to Agent, at the address indicated on the signature page hereof.

          (b) If to the Corporation, to:

Solexa Inc.

25861 Industrial Blvd.

Hayward, CA 94545

	or to such other address as a party may have been given notice by the other party in accordance
with this Section 19, but no such notice shall have been deemed given until actually received by
the party sought to be charged with the contents.

Page 6 of 6

 

     IN WITNESS WHEREOF, the parties hereto have executed this Agreement on and as of the day and
year first above written.

	 	 	 	 	 	 	 
	 	 	SOLEXA INC.
	 
	 	 	 	 	 	 
	 

	 	By:	 	/s/ Linda Rubinstein 	 	 
	 

	 	 	 	 

Linda Rubinstein
	 	 
	 
	 

	 	Title:
	 	Vice
President and Chief Financial Officer	 	 
	 

	 	 	 	(Title)	 	 
	 
	 	 	 	 	 	 
	 	 	AGENT:
	 
	 	 	 	 	 	 
	 

	 	By:	 	/s/ Joseph Whitters 	 	 
	 

	 	 	 	 

Joseph Whitters
	 	 
	 
	 	 	 	 	 	 
	 

	 	Address:	 	 	 	 
	 
	 	 	 	 	 	 
	 

	 	c/o Solexa,
	 	Inc.	 	 
	 

	 	25861	Industrial Blvd.	 	 
	 

	 	Hayward,
	 	CA 94545	 	 

Page 7 of 6

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