|Exhibit 31.1


CERTIFICATION OF CHIEF
EXECUTIVE OFFICER


(Pursuant to Rule 13a-14 of the
Securities 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 untrue statement of a
          material fact or omit to state a material fact necessary to make the statements
          made, in light of the circumstances under which such statements were made, not
          misleading with respect to the period covered by this report;


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


     4.    
          The registrants other certifying officers and I are responsible for
          establishing and maintaining disclosure controls and procedures (as defined in
          Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial
          reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the
          registrant and have:
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|a) | Designed such disclosure controls and procedures, or caused such disclosure
                    controls and procedures to be designed under our supervision, to ensure that
                    material information relating to the registrant, including its consolidated
                    subsidiaries, is made known to us by others within those entities, particularly
                    during the period in which this report is being prepared;
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|b) | Designed such internal control over financial reporting, or caused such
                    internal control over financial reporting to be designed under our supervision,
                    to provide reasonable assurance regarding the reliability of financial reporting
                    and the preparation of financial statements for external purposes in accordance
                    with generally accepted accounting principles;
|-- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

|c) | Evaluated the effectiveness of the registrants disclosure controls and
                    procedures and presented in this report our conclusions about the effectiveness
                    of the disclosure controls and procedures, as of the end of the period covered
                    by this report based on such evaluation; and
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|d) | Disclosed in this report any change in the registrants internal control
                    over financial reporting that occurred during the registrants most recent
                    fiscal quarter that has materially affected, or is reasonably likely to
                    materially affect, the registrants internal control over financial
                    reporting; and
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|5.    
          The registrants other certifying officers and I have disclosed, based on
          our most recent evaluation of internal control over financial reporting, to the
          registrants auditors and the audit committee of registrants board of
          directors (or persons performing the equivalent functions):
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|a) | All significant deficiencies and material weaknesses in the design or operation
                    of internal control over financial reporting which are reasonably likely to
                    adversely affect the registrants ability to record, process, summarize and
                    report financial information; and
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|b) | Any fraud, whether or not material, that involves management or other employees
                    who have a significant role in the registrants internal control over
                    financial reporting.
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Date: August 6, 2004

| |                                                                                                   
| | --------------------------------------------------------------------------------------------------
| | /s/Mark J. Emkjer
Mark J. EmkjerPresident and Chief Executive Officer(Principal Executive Officer)

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