<PAGE>

                                                                   Exhibit 10.38

                      PILOT PROJECT COLLABORATION AGREEMENT

         This Collaboration Agreement ("Agreement") is entered into as of
February 3rd, 2000 (the "Effective Date"), by and between Rosetta Inpharmatics,
Inc., ("Rosetta"), a corporation organized and existing under the laws of the
State of Delaware and having a place of business at 12040 - 115th Avenue
Northeast, Kirkland, Washington 98034-6900 and Monsanto Company and its
affiliates ("Monsanto"), a corporation organized and existing under the laws of
the State of Delaware and having a place of business at 800 North Lindbergh
Boulevard, St. Louis, Missouri 63167.

          The parties agree as follows:

         1. BASIS FOR AGREEMENT. Monsanto desires to conduct a pilot project
that will evaluate two aspects of Rosetta's technologies. One part of the
project will evaluate the Resolver-TM- Expression Data Analysis System
("Resolver-TM- System"). Rosetta and Monsanto both have possession of gene
expression data that will be used for evaluation of the Resolver. The second
part of the project will evaluate Rosetta's FlexJet-TM- microarray technology
including arrays ("F1exJet~ Arrays") and array design capabilities ("Array
Design"). For evaluation of the FlexJet~ Arrays and Array Design, Monsanto has
possession of gene sequence information that will be provided to Rosetta for the
construction of arrays and Monsanto has possession of nucleic acid material that
will be provided to Rosetta for hybridizing to microarrays ("Sample RNA").
Rosetta has expertise in the area of using microarrays and analyzing microarray
data to determine gene expression.

         The purpose of this Agreement is to set forth the terms and conditions
under which (a) Monsanto will evaluate the Resolver, (b) Rosetta will conduct
experiments using FlexJet-TM- Arrays constructed using sequence information
provided by Monsanto and hybridized with Sample RNA and provide Monsanto with an
analysis of the data generated from such experiments, (c) both parties will
evaluate the data generated, and (d) the conditions under which a follow-on
collaboration between Monsanto and Rosetta would take place.

         2. EVALUATION OF THE RESOLVER-TM- SYSTEM. Monsanto employees will
come to Rosetta's premises to use and evaluate the Resolver-TM- system for
analysis of multiple data types at a time to be agreed between the parties.
The timing for this evaluation will be dependent upon the availability of
data under Section 2.4 below. The parties agree that the Resolver-TM- System
evaluation session will involve up to [***] Monsanto employees who will
attend the evaluation concurrently. [***] of Rosetta personnel time will be
included for the evaluation session as hosts/guides. The following data types
will be analyzed as part of the evaluation:

                  2.1 ANALYSIS OF SINGLE CHANNEL DATA FROM ROSETTA. For this
purpose a yeast Genome Reporter Matrix (GRM) compound database containing at
least 500 different compound and mutant profiles will be used to analyze
`single channel' data in the Resolver-TM- System. The use of these data in
this evaluation is intended to demonstrate the applicability of
single-channel data for database construction, and the flexibility of the
Resolver-TM- System in analysis of such data.

                  2.2 ANALYSIS OF DUAL CHANNEL DATA FROM ROSETTA. For this
purpose a Rosetta cDNA array-based compendium of mutant and compound-treated
profiles will be utilized. The use of these data in this hands-on evaluation is
intended to demonstrate the applicability of dual-channel data for database
construction, and the flexibility of the Resolver-TM- System in analysis of such
data.

                  2.3 [***]


*   Material has been omitted pursuant to a request for confidential treatment,
    and such material has been filed separately with the SEC.

<PAGE>

                  2.4 ANALYSIS OF MONSANTO INK JET DATA. Up to 100 (one
hundred) sets of FlexJet-TM- Array data will be loaded into Resolver-TM- from
the Monsanto evaluation set of data that will be generated as part of the
evaluation of Rosetta's FlexJet-TM- Technology under this Agreement.

         3. EVALUATION OF FLEXJET-TM- TECHNOLOGV. The purpose of this part of
the pilot project is to evaluate the Rosetta ink jet microarray technology
for use in gene expression analysis in several species. This evaluation will
involve design and utilization of a multi-species array as follows:

                  3.1 [***]

                           3.1.1 [***]

                           3.1.2 [***]

                           3.1.3 [***]

                  3.2 [***]

                           3.2.1 [***]

                           3.2.2 [***]

                           3.2.3 [***]

*   Material has been omitted pursuant to a request for confidential treatment,
    and such material has been filed separately with the SEC.

                                      -2-
<PAGE>

                           3.2.4 [***]

                  3.3 FABRICATION OF SAA. Within 15 (fifteen) business days of
receipt of all the Sequence Information by Rosetta and notification from
Monsanto of the genes to be represented on the SAA, Rosetta shall employ
commercially reasonable efforts to begin fabrication of SAAs that will be used
in this project.

                  3.4 SAA HYBRIDIZATIONS. Monsanto will provide whole RNA
samples to Rosetta ("Sample RNA"). All array hybridizations will be carried out
at Rosetta using a 2-color system to monitor relative expression in two (2) RNA
samples within four (4) weeks of receipt of the last RNA sample from Monsanto,
assuming that such receipt date is after initiation of the SAA fabrication.
Details of the samples, and hybridizations can be found in Appendix B --
Hybridizations Carried Out by Rosetta. This will result in a total of [***]
F1exJet~ Arrays being used in experiments. The experimental data
resulting from the hybridizations ("Array Data") will be loaded into the
Resolver~' System for analysis.

                  3.5 SUPPLY OF THE SAMOLE RNA. Sample RNA will be in the form
of whole RNA in matched sample pairs. The procedures to be used by Monsanto for
providing Sample RNA to Rosetta are set forth in Appendix C -- Sample RNA
Provided by Monsanto.

                  3.6 ANALYZED DATA DELIVERED TO MONSANTO. Information that is
the result of the microarray experiments performed by Rosetta under this
Agreement in analyzed form shall be termed herein the "Analyzed Data." The
Analyzed Data shall be disclosed in a written report to Monsanto within [***]
business days after completion of the last hybridization. Array Data
associated with Analyzed Data will be provided to Monsanto in Monsanto specified
TAB deliminated text files via compact disc.

          4. JOINT EVALUATION MEETING. Within [***] business days of
completion of the experiments conducted to evaluate Rosetta's Resolver-TM-
System and FlexJet-TM- Technology, Rosetta and Monsanto will meet to
determine whether the results of the pilot project fulfilled the pre-defined
success criteria. The criteria that will be used to determine success or
failure of the pilot project are set forth below.

                  4.1 EVALUATION OF RESOLVER-TM- SYSTEM. That the Resolver-TM-
System compares favorably with other array data analysis packages and
effectively meets the analysis needs of Monsanto.

                  4.2 EVALUATION OF FLEXJET-TM- TECHNOLOGY. The following
criteria will be used:

                           4.2.1 Expression values reported by the FlexJet-TM-
Technology are at least as accurate and reproducible as alternative array
technologies. Monsanto personnel will present data pertaining to the relative
accuracy of the FlexJet-TM- technology as compared to the alternative
technologies.

          5. [***]

*   Material has been omitted pursuant to a request for confidential treatment,
    and such material has been filed separately with the SEC.

                                      -3-
<PAGE>

         6. QUALITY CONTROL. To determine whether failed results of a microarray
experiment are the result of Rosetta's procedures or the Sequence Information or
Sample RNA provided by Monsanto, the procedures Set forth in Appendix C under
"Quality of Sample RNA" will be followed.

         7. RETURN OF UNUSED REAGENTS. All Sample RNA provided by Monsanto that
are not used by Rosetta shall be returned to Monsanto or destroyed, at
Monsanto's discretion.

         8. COMPENSATION. As compensation for Rosetta's contributions for
conducting the pilot project, Monsanto will pay Rosetta a non-refundable sum of
[***]

         The remaining [***] shall be paid on completion of the pilot project.

         9. TERM AND TERMINATION. This Agreement may expire or be terminated, as
follows:

                  9.1. COMPLETION OF WORK. This Agreement shall expire upon
completion of the pilot project which shall be after the meeting(s) set forth in
Section 4. Details of the anticipated timeframe for this agreement can be found
in Appendix D -- Statement of Work for the Monsanto/Rosetta Pilot Agreement.

                  9.2 BY BREACH. In the event either party shall materially
breach any of the terms, conditions and agreements contained in this Agreement
to be kept, observed and performed by it, then the other party may terminate
this Agreement, at its option and without prejudice to any of its other legal
and equitable rights and remedies, by giving the party who committed the breach
[***] notice in writing, particularly specifying the breach, unless the notified
party within such [***] period shall have rectified the breach.

         10.      INTELLECTUAL PROPERTY AND HANDLING OF INFORMATION AND DATA.

                  10.1 EVALUATION OF RESOLVER-TM- SYSTEM. Based upon use of
the Resolver-TM- System in analyzing Monsanto and Rosetta data, the parties
agree that the following will apply.

                           10.1.1 [***]

                           10.1.2 Specific details of the generation,
constituent parts, and implementation of error models generated for [***] will
be solely owned by [***] and will not be communicated to [***] personnel.

                           10.1.3 Any discoveries (independent of the generation
of an error model) made by [***] personnel utilizing [***] data in the
Resolver-TM- System shall be owned by [***].

                  10.2 EVALUATION OF FLEXJET-TM- TECHNOLOGY. The following will
apply to information,

*   Material has been omitted pursuant to a request for confidential treatment,
    and such material has been filed separately with the SEC.

                                      -4-
<PAGE>

data, discoveries, and inventions related to this evaluation.

                           10.2.1 All Monsanto sequence data shall remain the
property of Monsanto and proprietary to it, and as such Rosetta shall ensure the
security of all such information.

                           10.2.2 All proprietary Monsanto sequence data will be
permanently removed from Rosetta storage devices at the conclusion of the pilot
project

                           10.2.3 Specific details of the parameters and
techniques used in oligonucleotide set selection and the oligonucleotide
sequences used will not be disclosed to Monsanto nor shall Rosetta disclose this
information to any third party.

                           10.2.4 Rosetta shall not use oligonucleotides
designed using Monsanto proprietary Sequence Information in future array
designs. However, this restriction shall not prevent Rosetta from independently
creating the same oligonucleotide or make arrays for the same Sequence
Information if such same Sequence Information is provided independently by a
third party in the future.

                           10.2.5 During the pilot project, all arrays will be
fabricated and hybridized at Rosetta.

                           10.2.6 [***]

                           10.2.7 Specific details of the generation,
constituent parts, and implementation of error models generated for SAAs will be
solely owned by Rosetta and will not be communicated to Monsanto personnel.

         11. CONFIDENTIAL INFORMATION. For the purposes of this Agreement, the
term "Confidential Information" shall mean, and collectively include, all
non-public information relating to the business, plans and/or technology of
either party including, but not limited to, this Agreement, technical
information including inventions, methods, plans, processes, specifications,
source code, object code, characteristics, raw data, equipment design, know-how,
experience, and trade secrets, developmental, marketing, sales, operating,
performance, and cost information; computer programming techniques; information
relating to the Sample RNA, designed oligonucleotides, Array Data, and Analyzed
Data; and all record bearing media containing or disclosing the foregoing
information and techniques including written business plans, patents and patent
applications, grant applications, notes, and memoranda, whether in writing or
presented, stored or maintained in or by electronic, magnetic, or other means,
to the extent that such information (a) as of the date of disclosure by the
disclosing party to the receiving party, was not known to the receiving party as
evidenced by written documentation, (b) was not disclosed in published
literature or otherwise generally available to the public, (c) became generally
available to the public after the date of disclosure, (d) was obtained from a
third party without binder of secrecy, provided, however, that such third party
has no confidentiality obligations to the disclosing party or any of its
affiliates or (e) is at any time independently developed by employees or agents
of the receiving party who have had no access to or use of such information.

                  11.1 Rosetta agrees that Sample RNA, designed
oligonucleotides, Array Data and Analyzed Data constitute highly Confidential
Information of Monsanto. [***]

*   Material has been omitted pursuant to a request for confidential treatment,
    and such material has been filed separately with the SEC.

                                      -5-
<PAGE>

                  11.2 RESTRICTIONS ON USE AND DISCLOSURE OF CONFIDENTIAL
INFORMATION.

                           11.2.1 The receiving party agrees to treat as
confidential and not to use other than to perform this Agreement, and not to
reverse engineer or decompile any Confidential Information disclosed to it by
the disclosing party. The receiving party agrees not to disclose to any third
party any Confidential Information disclosed to it by the disclosing party. The
receiving party further covenants that it will exercise every reasonable
precaution to preclude the unauthorized disclosure by any of its personnel or
employees to third parties of any Confidential Information disclosed to it by
the disclosing party under the provisions of this Agreement. The receiving party
agrees not to disclose the Confidential Information it receives from the
disclosing party to anyone except its own personnel and employees, who (a) are
actively and directly evaluating the Confidential Information, and consequently
need to know such information and (b) are bound by confidentiality,
nondisclosure, and nonuse obligations at least as stringent as those set forth
in this paragraph 11.2.1.

                           11.2.2 The obligations of paragraph 11.2.1 hereof
will expire with respect to each item of Confidential Information [***] from
the termination date of this Agreement.

                           11.2.3 Notwithstanding the obligations of paragraph
11.2.1, the receiving party shall be permitted to disclose Confidential
Information that is required to be disclosed by the receiving party to comply
with applicable laws, court order, or governmental regulations, provided that
the receiving party provides prior written notice of such disclosure to the
disclosing party and takes reasonable and lawful actions to avoid and/or
minimize the degree of such disclosure. The prior written notice must be given
in sufficient time to permit the disclosing party to seek a protective order or
some other accommodation to protect the confidentiality of the information.

                  11.3 TERMS OF THIS AGREEMENT. The parties will keep the terms
of this Agreement confidential and not disclose them to any third party other
than affiliates which the party has an interest in of at least a fifty percent,
except as may be required by regulatory agencies or courts or as required by
law, and will then use all reasonable and lawful actions to keep the terms of
this Agreement confidential. The party required to make such disclosure will
provide sufficient prior written notice about such disclosure to the other party
to allow the other party to review the form of the disclosure and make requested
revisions or modifications if possible.

          12. DISCLAIMER OF REPRESENTATIONS AND WARRANTIES. NEITHER PARTY MAKES
ANY REPRESENTATIONS OR EXTENDS ANY WARRANTIES, EXPRESS OR IMPLIED, AS TO ANY
MA1TER WHATSOEVER INCLUDING, WITHOUT LIMITATION, THE SAMPLE RNA, THE ARRAY DATA,
OR THE ANALYZED DATA INCLUDING, BUT NOT LIMITED TO, WARRANTIES OF OWNERSHIP,
MERCHANTABILITY, OR FITNESS FOR A PARTICULAR PURPOSE. Without limitation of the
foregoing generality, nothing contained herein or in any disclosure of research
conducted by Rosetta shall be construed as extending any representation or
warranty with respect to research using Sample RNA or the results to be obtained
by the use thereof or any products resulting therefrom, or that use of the Array
Data or Analyzed Data will be free from infringement of patents or other
proprietary rights of third parties. Neither party makes any warranties
whatsoever as to the commercial or scientific value of the Array Data or
Analyzed Data. NOTWITHSTANDING ANYTHING HEREIN TO THE CONTRARY, MONSANTO
REPRESENTS AND WARRANTS

*   Material has been omitted pursuant to a request for confidential treatment,
    and such material has been filed separately with the SEC.

                                      -6-
<PAGE>

THAT IT HAS THE RIGHT TO TRANSFER THE SAMPLE RNA TO ROSETTA ON THE TERMS AND
CONDITIONS OF THIS AGREEMENT.

          13. SURVIVAL OF OBLIGATIONS. The rights and obligations of Sections
10, 11, and 12 shall survive expiration or termination of this Agreement.

          14. NO OBLIGATION TO LICENSE. Nothing contained herein shall be
construed by implication or otherwise (a) so as to obligate either of the
parties to enter into an agreement for purchase of or license to any products,
technology, or services; or (b) as the grant of any right or license by either
party to any Confidential Information or any intellectual property rights,
except as set forth in this Agreement.

          15. ASSIGNMENT This Agreement may be assigned or transferred by
Monsanto to the acquirer of substantially all of the assets of Monsanto relating
to this Agreement.

          16. GENERAL PROVISIONS. The following general provisions shall apply
to this Agreement:

                  16.1 NOTICES. All notices and communications provided for
hereunder shall be in writing and shall be mailed, faxed, or otherwise delivered
to the business address or fax number of the respective parties set forth below,
or to such other address or fax number as either party shall designate in
writing to the other.

      -       If to Rosetta:            Rosetta Inpharmatics
                                        12040- 115th Avenue NE
                                        Kirkland, WA 98034
                                        Attention: Chief Operating Officer

              If to Monsanto            Monsanto Company
                                        800 North Lindbergh Blvd
                                        St. Louis, Missouri, 63167

                                        Attention: Vice President, Genomics
                                        Technologies

                  16.2 BENEFITS. All terms and provisions of this Agreement
shall bind and inure to the benefit of the parties hereto, and upon their
respective successors and assigns.

                  16.3 COUNTERPARTS. This Agreement may be executed
simultaneously in one or more counterparts, each of which shall be deemed to be
original but all of which together shall constitute one and the same Agreement.

                  16.4 CONSTRUCTION AND INTERPRETATION. This Agreement shall be
construed and fairly interpreted in accordance with its terms, without any
strict construction in favor of or against either party. Ambiguities shall not
be interpreted against the drafting party. Any ambiguities in this Agreement
shall be interpreted in accordance with the objectives stated in Section 1. In
construing or interpreting this Agreement, the word "or" shall not be construed
as exclusive, and the word "including" shall not be limiting. The use of the
singular or plural form shall include the other form and the use of the
masculine, feminine or neuter gender shall include the other genders. All
captions and headings in this Agreement are for convenience only and shall not
be considered as substantive parts of this Agreement or determinative in the
interpretation of this Agreement.

                  16.5 ENTIRE UNDERSTANDING. This Agreement constitutes the
entire understanding between the parties hereto with respect to the subject
matter hereof. No modifications, extensions or


                                      -7-
<PAGE>

waiver of any provisions hereof or release of any right hereunder shall be
valid, unless the same is in writing and is consented to by both parties hereto.

                  16.6 CHOICE OF LAW. This Agreement shall be governed by the
laws of the State of Washington, excluding choice of law principles that would
cause the law of any other jurisdiction to apply.

                  16.7 AMENDMENT. This Agreement may be amended only by a
written agreement signed by both Parties hereto.

                  16.8 WAIVER. Waiver of any provision of this Agreement shall
not be deemed a waiver of any other provision of this Agreement.

                  16.9 FORCE MAJEURE. The failure of any party to perform
hereunder as a result of governmental action, laws, orders, or regulations, or
as a result of events, such as war, acts of public enemies, fires, floods,
earthquakes, acts of God or any causes of like kind beyond the reasonable
control of such party is excused for so long as such cause exists, but only to
the extent such failure is caused by. such law, order, regulation, or event.

                            [Signature Page Follows]


                                      -8-
<PAGE>

                  IN WITNESS WHEREOF, the parties hereto have caused their duly
authorized representatives to execute this Agreement as of the date and year
first written above.

MONSANTO COMPANY                         ROSETTA INPHARMATICS, INC.


By /s/ SLOAN RAUSSER                     By /s/ JOHN J. KING, II
  -----------------------------             ------------------------------------

SLOAN RAUSSER                            JOHN J. KING, II
---------------------------------            -----------------------------------
         Print Name                              Print Name

DIRECTOR, BUSINESS DEVELOPMENT           SR. VICE PRESIDENT, CHIEF OPERATING
                                         OFFICER
---------------------------------        ---------------------------------------
          Title                                           Title

2/3/00                                   2/1/00
---------------------------------        ---------------------------------------
         Date                                        Date


                                      -9-
<PAGE>

                         APPENDIX A -- DESIGN OF THE SAA

[***]





*   Material has been omitted pursuant to a request for confidential treatment,
    and such material has been filed separately with the SEC.

                                      A-1

<PAGE>


               APPENDIX B - HYBRIDIZATIONS CARRIED OUT BY ROSETTA

[***]





*   Material has been omitted pursuant to a request for confidential treatment,
    and such material has been filed separately with the SEC.

                                      A-2

<PAGE>


                    APPENDIX C -- SAMPLE RNA PROVIDED BY MONSANTO

[***]





*   Material has been omitted pursuant to a request for confidential treatment,
    and such material has been filed separately with the SEC.

                                      A-6


<PAGE>

         APPENDIX D -- STATEMENT OF WORK FOR THE MONSANTO/ROSETTA PILOT

[***]





*   Material has been omitted pursuant to a request for confidential treatment,
    and such material has been filed separately with the SEC.


                                      A-7