**Exhibit31.1**

**CERTIFICATIONOF CHIEF EXECUTIVE OFFICER**

**(Pursuantto Rule 13a-14(a) of theSecurities Exchange Act of 1934, as amended,as Adopted Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002)**

I, Mark J. Emkjer,certify that:

1.      I have reviewed this quarterly report on Form 10-Q of Accelrys,Inc.;

2.      Based on my knowledge, this report does not contain any untruestatement of a material fact or omit to state a material fact necessary to makethe statements made, in light of the circumstances under which such statementswere made, not misleading with respect to the period covered by this report;

3.      Based on my knowledge, the financial statements, and otherfinancial information included in this report, fairly present in all materialrespects the financial condition, results of operations and cash flows of theregistrant as of, and for, the periods presented in this report;

4.      The registrant’s other certifying officer and I are responsiblefor establishing and maintaining disclosure controls and procedures (as definedin Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control overfinancial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f))for the registrant and have:

a)           Designed suchdisclosure controls and procedures, or caused such disclosure controls andprocedures to be designed under our supervision, to ensure that materialinformation relating to the registrant, including its consolidatedsubsidiaries, is made known to us by others within those entities, particularlyduring the period in which this report is being prepared;

b)          Designed such internalcontrol over financial reporting, or caused such internal control overfinancial reporting to be designed under our supervision, to provide reasonableassurance regarding the reliability of financial reporting and the preparationof financial statements for external purposes in accordance with generallyaccepted accounting principles;

c)           Evaluated theeffectiveness of the registrant’s disclosure controls and procedures and presentedin this report our conclusions about the effectiveness of the disclosurecontrols and procedures, as of the end of the period covered by this reportbased on such evaluation; and

d)          Disclosed in this reportany change in the registrant’s internal control over financial reporting thatoccurred during the registrant’s most recent fiscal quarter that has materiallyaffected, or is reasonably likely to materially affect, the registrant’sinternal control over financial reporting; and

5.      The registrant’s other certifying officer and I have disclosed,based on our most recent evaluation of internal control over financialreporting, to the registrant’s auditors and the audit committee of theregistrant’s board of directors (or persons performing the equivalentfunctions):

a)           All significantdeficiencies and material weaknesses in the design or operation of internalcontrol over financial reporting which are reasonably likely to adverselyaffect the registrant’s ability to record, process, summarize and reportfinancial information; and

b)          Any fraud, whether ornot material, that involves management or other employees who have asignificant role in the registrant’s internal control over financial reporting.

Date:  October 27, 2006
|        |   | /s/ Mark J. Emkjer                    |   |
|--------|--------|---------------------------------------|--------|
|   |   | Mark J. Emkjer                        |   |
|   |   | President and Chief Executive Officer |   |
|   |   | (Principal Executive Officer)         |   |

 

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