UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549

                                  SCHEDULE 13D
                        Under the Securities Act of 1934
                                (Amendment No. 2)

                         BROOKS AUTOMATION, INC. (BRKS)
                                (Name of Issuer)

                                  Common Stock
                         (Title of Class of Securities)

                                    114340102
                                 (CUSIP Number)

                                David Nierenberg

                               The D3 Family Funds

                               19605 NE 8th Street

                                 Camas, WA 98607

                                  360-604-8600

                  (Name, Address and Telephone Number of Person
                Authorized to Receive Notices and Communications)

                                November 17, 2005
             (Date of Event which Requires Filing of this Statement)

If the filing person has previously  filed a statement on Schedule 13G to report
the  acquisition  that is the  subject of this  Schedule  13D and is filing this
schedule because of ss.ss.240.13d-1(e),  240.13d-1(f) or 240.13d-1(g), check the
following box: |_|



--------------------------------------------------------------------------------
1    NAME OF REPORTING PERSON
     S.S. OR I.R.S. IDENTIFICATION NOS. OF ABOVE PERSON

     The D3 Family Fund, L.P. (David Nierenberg is president
     of the General Partner, which is Nierenberg Investment
     Management Company.)
--------------------------------------------------------------------------------
2    CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                                 (a)  |X|
                                                                 (b)  |_|
--------------------------------------------------------------------------------
3    SEC USE ONLY


--------------------------------------------------------------------------------
4    SOURCE OF FUNDS* 

     WC
--------------------------------------------------------------------------------
5    CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED
     PURSUANT TO ITEMS 2(d) OR 2(e)                                   |_|


--------------------------------------------------------------------------------
6    CITIZENSHIP OR PLACE OF ORGANIZATION

     Washington
--------------------------------------------------------------------------------
               7    SOLE VOTING POWER

                    1,527,032 common shares (2.0%)
               -----------------------------------------------------------------
  NUMBER OF    8    SHARED VOTING POWER
   SHARES
BENEFICIALLY        0
  OWNED BY     -----------------------------------------------------------------
    EACH       9    SOLE DISPOSITIVE POWER
  REPORTING
   PERSON           1,527,032
    WITH       -----------------------------------------------------------------
               10   SHARED DISPOSITIVE POWER

                    0
--------------------------------------------------------------------------------
11   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

     3,148,802 shares (4.2%)
--------------------------------------------------------------------------------
12   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES*  |_|


--------------------------------------------------------------------------------
13   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)

     4.2%
--------------------------------------------------------------------------------
14   TYPE OF REPORTING PERSON*

     PN
--------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!


                                       2


--------------------------------------------------------------------------------
1    NAME OF REPORTING PERSON
     S.S. OR I.R.S. IDENTIFICATION NOS. OF ABOVE PERSON

     The D3 Family Retirement Fund, L.P. (David Nierenberg is president of the
     General Partner, which is Nierenberg Investment Management Company.)
--------------------------------------------------------------------------------
2    CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                                 (a)  |X|
                                                                 (b)  |_|
--------------------------------------------------------------------------------
3    SEC USE ONLY


--------------------------------------------------------------------------------
4    SOURCE OF FUNDS*

     WC
--------------------------------------------------------------------------------
5    CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED
     PURSUANT TO ITEMS 2(d) OR 2(e)                                   |_|


--------------------------------------------------------------------------------
6    CITIZENSHIP OR PLACE OF ORGANIZATION

     Washington
--------------------------------------------------------------------------------
               7    SOLE VOTING POWER

                    454,000 common shares (0.6%)
               -----------------------------------------------------------------
  NUMBER OF    8    SHARED VOTING POWER
   SHARES
BENEFICIALLY        0
  OWNED BY     -----------------------------------------------------------------
    EACH       9    SOLE DISPOSITIVE POWER
  REPORTING
   PERSON           454,000
    WITH       -----------------------------------------------------------------
               10   SHARED DISPOSITIVE POWER

                    0
--------------------------------------------------------------------------------
11   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

     3,148,802 shares (4.2%)
--------------------------------------------------------------------------------
12   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES*  |_|


--------------------------------------------------------------------------------
13   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)

     4.2%
--------------------------------------------------------------------------------
14   TYPE OF REPORTING PERSON*

     PN
--------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!


                                       3


--------------------------------------------------------------------------------
1    NAME OF REPORTING PERSON
     S.S. OR I.R.S. IDENTIFICATION NOS. OF ABOVE PERSON

     The D3 Children's Fund, L.P. (David Nierenberg is president of the General
     Partner, which is Nierenberg Investment Management Company.)
--------------------------------------------------------------------------------
2    CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                                 (a)  |X|
                                                                 (b)  |_|
--------------------------------------------------------------------------------
3    SEC USE ONLY


--------------------------------------------------------------------------------
4    SOURCE OF FUNDS* 

     WC
--------------------------------------------------------------------------------
5    CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED
     PURSUANT TO ITEMS 2(d) OR 2(e)                                   |_|


--------------------------------------------------------------------------------
6    CITIZENSHIP OR PLACE OF ORGANIZATION

     Washington
--------------------------------------------------------------------------------
               7    SOLE VOTING POWER

                    116,360 common shares (0.2%)
               -----------------------------------------------------------------
  NUMBER OF    8    SHARED VOTING POWER
   SHARES
BENEFICIALLY        0
  OWNED BY     -----------------------------------------------------------------
    EACH       9    SOLE DISPOSITIVE POWER
  REPORTING
   PERSON           116,360
    WITH       -----------------------------------------------------------------
               10   SHARED DISPOSITIVE POWER

                    0
--------------------------------------------------------------------------------
11   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

     3,148,802 shares (4.2%)
--------------------------------------------------------------------------------
12   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES*  |_|


--------------------------------------------------------------------------------
13   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)

     4.2%
--------------------------------------------------------------------------------
14   TYPE OF REPORTING PERSON*

     PN
--------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!


                                       4


--------------------------------------------------------------------------------
1    NAME OF REPORTING PERSON
     S.S. OR I.R.S. IDENTIFICATION NOS. OF ABOVE PERSON

     The D3 Offshore Fund, L.P. (David Nierenberg is president of the General
     Partner, which is Nierenberg Investment Management Company.)
--------------------------------------------------------------------------------
2    CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                                 (a)  |X|
                                                                 (b)  |_|
--------------------------------------------------------------------------------
3    SEC USE ONLY


--------------------------------------------------------------------------------
4    SOURCE OF FUNDS* 

     WC
--------------------------------------------------------------------------------
5    CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED
     PURSUANT TO ITEMS 2(d) OR 2(e)                                   |_|


--------------------------------------------------------------------------------
6    CITIZENSHIP OR PLACE OF ORGANIZATION

     Bahamas
--------------------------------------------------------------------------------
               7    SOLE VOTING POWER

                    750,160 common shares (1.0%)
               -----------------------------------------------------------------
  NUMBER OF    8    SHARED VOTING POWER
   SHARES
BENEFICIALLY        0
  OWNED BY     -----------------------------------------------------------------
    EACH       9    SOLE DISPOSITIVE POWER
  REPORTING
   PERSON           750,160
    WITH       -----------------------------------------------------------------
               10   SHARED DISPOSITIVE POWER

                    0
--------------------------------------------------------------------------------
11   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

     3,148,802 shares (4.2%)
--------------------------------------------------------------------------------
12   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES*  |_|


--------------------------------------------------------------------------------
13   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)

     4.2%
--------------------------------------------------------------------------------
14   TYPE OF REPORTING PERSON*

     PN
--------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!


                                       5


--------------------------------------------------------------------------------
1    NAME OF REPORTING PERSON
     S.S. OR I.R.S. IDENTIFICATION NOS. OF ABOVE PERSON

     The D3 Family Bulldog Fund, L.P. (David Nierenberg is
     president of the General Partner, which is Nierenberg
     Investment Management Company.)
--------------------------------------------------------------------------------
2    CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP*
                                                                 (a)  |X|
                                                                 (b)  |_|
--------------------------------------------------------------------------------
3    SEC USE ONLY


--------------------------------------------------------------------------------
4    SOURCE OF FUNDS* 

     WC
--------------------------------------------------------------------------------
5    CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED
     PURSUANT TO ITEMS 2(d) OR 2(e)                                   |_|


--------------------------------------------------------------------------------
6    CITIZENSHIP OR PLACE OF ORGANIZATION

     Washington
--------------------------------------------------------------------------------
               7    SOLE VOTING POWER

                    301,250 common shares (0.4%)
               -----------------------------------------------------------------
  NUMBER OF    8    SHARED VOTING POWER
   SHARES
BENEFICIALLY        0
  OWNED BY     -----------------------------------------------------------------
    EACH       9    SOLE DISPOSITIVE POWER
  REPORTING
   PERSON           301,250
    WITH       -----------------------------------------------------------------
               10   SHARED DISPOSITIVE POWER

                    0
--------------------------------------------------------------------------------
11   AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON

     3,148,802 shares (4.2%)
--------------------------------------------------------------------------------
12   CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES*  |_|


--------------------------------------------------------------------------------
13   PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)

     4.2%
--------------------------------------------------------------------------------
14   TYPE OF REPORTING PERSON*

     PN
--------------------------------------------------------------------------------
                     *SEE INSTRUCTIONS BEFORE FILLING OUT!


                                       6


Item 1. Security and Issuer.

        Common stock in BROOKS AUTOMATION, INC. (BRKS) 15 Elizabeth Drive,
        Chelmsford, MA 01824-4111.

Item 2. Identity and Background.

        The D3 Family Funds are  Washington  State limited  partnerships,  whose
        principal  business is  investing  in the  equities of public  micro-cap
        issuers.  The D3 Family Funds consist of: D3 Family Fund, L.P, D3 Family
        Retirement  Fund, L.P, D3 Children's  Fund, L.P, D3 Offshore Fund, L.P.,
        D3 Family  Bulldog  Fund,  L.P.  Located at 19605 N.E.  8th St.,  Camas,
        Washington  98607.  No  convictions  or  administrative  proceedings  as
        described in 2 (d) and (e).

Item 3. Source and Amount of Funds or Other Consideration

        Source of funds is money invested in the partnership by their partners.

Item 4. Purpose of Transaction

        Solely as a result of Brooks' recent acquisition of Helix Technology for
        Brooks' stock,  our ownership  percentage of Brooks has fallen below the
        5% filing  threshold.  We do want to point  out,  however,  that,  since
        filing our prior 13D we have bought 577,646 more shares of Brooks.

        We have made these additional  purchases  because we continue to believe
        that  Brooks  is  extremely   undervalued   using  almost  any  relevant
        definition  of value:  relative to the  company's  long term revenue and
        earnings  growth  potential,  relative  to  its  strong  balance  sheet,
        relative  to  its  leading  competitive   position  in  outsourced  tool
        automation systems and service,  relative to the increasing  penetration
        of tool outsourcing, and relative to its complete and capable management
        team.

        We attribute the  persistence of Brooks'  undervaluation  to three short
        term factors,  all of which we expect to decline in importance  over the
        coming months. First, some Helix shareholders  currently are selling the
        Brooks  shares  they  received in exchange  for their Helix  shares.  We
        believe  this is  happening  either  because  they earned an  acceptable
        return  on their  Helix  investment  or  because  they  only  invest  in
        companies which pay dividends,  which Brooks does not.  Second,  Brooks'
        software  division  recently  surprised and  disappointed  the financial
        community with weak sales and an operating  loss.  Corporate  management
        moved quickly to downsize the software  division and narrow  sharply its
        strategic  focus,  which had been  overbroad.  We expect  immediate  and
        substantial  improvement in the operating performance of Brooks Software
        and further expect that it soon will become, as before, an opportunistic
        source of positive cash for the parent. More


                                       7


        important,  though,  is that Brooks'  acquisition of Helix makes crystal
        clear that the parent's strategic focus is on outsourced tool automation
        systems and services.  Third, some market pundits have been predicting a
        poor retail Christmas,  projecting from that, weak consumer  electronics
        sales,   flagging  demand  for  chips,   and  diminished   appetite  for
        semiconductor  capital  equipment.  To  which we  respond,  based on our
        differing  assessment  of  how  well  consumer  electronics  seem  to be
        selling: "Bah, Humbug!"

        We do have a second  reason for  amending our 13D,  beyond  updating our
        ownership numbers. Immediately before Thanksgiving,  we sent a letter to
        the Chair of the Nominating and Governance Committee of Brooks' Board of
        Directors,  setting  forth our views on  several  matters  of  corporate
        governance.  Unlike many other activist hedge funds, which seem to enjoy
        using their letters as rhetorical  weapons, we have no plans to take our
        letter   public.    Diplomatic    negotiations    are   best   conducted
        diplomatically.  Moreover,  our relationship with Brooks is anything but
        adversarial.  In fact,  we are  very  pleased  with  their  most  recent
        addition  to the board,  which we view as  extremely  responsive  to our
        concerns.  Our only reason for disclosing the existence of our letter is
        that we believe that relevant federal regulations obligate us to do so.

Item 5. Interest in Securities of the Issuer.

        (a,b)   D3 Family Funds own and have sole voting and  dispositive  power
                over 3,148,802, 4.2% common shares of BRKS.

        (c)



           Fund                              Transaction Date      Shares Bought  Price
                                                                 
           D3 Family Fund, L.P.                 10/11/2005             45,000     12.72
           D3 Family Fund, L.P.                 10/27/2005             70,000     11.99
           D3 Family Fund, L.P.                 10/28/2005             17,700     11.64
           D3 Family Retirement Fund, L.P.      10/11/2005             20,000     12.72
           D3 Childrens Fund, L.P.              10/28/2005             12,000     11.64
           D3 Offshore Fund, L.P.               10/11/2005             30,000     12.72
           D3 Offshore Fund, L.P.               10/27/2005             42,500     11.99
           D3 Family Bulldog Fund, L.P.         10/11/2005              5,000     12.72
           D3 Family Bulldog Fund, L.P.         10/27/2005             50,000     11.99
           D3 Family Bulldog Fund, L.P.         10/28/2005             25,000     11.64


        (d)     N/A

        (e)     N/A


                                       8


Item 6. Contracts, Arrangements, Understandings or Relationships with Respect to
        Securities of the Issuer.

        N/A

Item 7. Material to be Filed as Exhibits

        N/A

                                    SIGNATURE

After reasonable inquiry and to the best of my knowledge and belief, each of the
undersigned certifies that the information set forth in the Statement is true,
complete and correct.

December 9, 2005                        /s/ DAVID NIERENBERG
                                        ----------------------------------------
                                        David Nierenberg
                                        President
                                        Nierenberg Investment Management
                                        Company, Inc., the General Partner of
                                        The D3 Family Funds


                                       9