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Codexis, Inc. – ‘10-K’ for 12/31/20 – ‘EX-101.CAL’

On:  Monday, 3/1/21, at 4:58pm ET   ·   For:  12/31/20   ·   Accession #:  1200375-21-21   ·   File #:  1-34705

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  As Of               Filer                 Filing    For·On·As Docs:Size

 3/01/21  Codexis, Inc.                     10-K       12/31/20  110:14M

Annual Report   —   Form 10-K
Filing Table of Contents

Document/Exhibit                   Description                      Pages   Size 

 1: 10-K        Annual Report                                       HTML   1.94M 
 2: EX-23.1     Consent of Expert or Counsel                        HTML     29K 
 3: EX-31.1     Certification -- §302 - SOA'02                      HTML     33K 
 4: EX-31.2     Certification -- §302 - SOA'02                      HTML     33K 
 5: EX-32.1     Certification -- §906 - SOA'02                      HTML     31K 
12: R1          Cover Page                                          HTML     93K 
13: R2          Consolidated Balance Sheets                         HTML    139K 
14: R3          Consolidated Balance Sheets (Parenthetical)         HTML     46K 
15: R4          Consolidated Statements of Operations               HTML     78K 
16: R5          Consolidated Statements Stockholders' Equity        HTML     89K 
17: R6          Consolidated Statements of Stockholders' Equity     HTML     40K 
                (Parenthetical)                                                  
18: R7          Consolidated Statements of Cash Flows               HTML    119K 
19: R8          Description of Business                             HTML     56K 
20: R9          Basis of Presentation and Summary of Significant    HTML    122K 
                Accounting Policies                                              
21: R10         Revenue Recognition                                 HTML    116K 
22: R11         Net Loss per Share                                  HTML     36K 
23: R12         Collaborative Arrangements                          HTML     74K 
24: R13         Investments in Non-Marketable Securities            HTML     40K 
25: R14         Fair Value Measurements                             HTML     49K 
26: R15         Balance Sheets Details                              HTML     71K 
27: R16         Stock-based Compensation                            HTML    176K 
28: R17         Capital Stock                                       HTML     33K 
29: R18         401(k) Plan                                         HTML     34K 
30: R19         Income Taxes                                        HTML    116K 
31: R20         Commitments and Contingencies                       HTML     87K 
32: R21         Related Party Transactions                          HTML     37K 
33: R22         Segment, Geographical and Other Revenue             HTML    163K 
                Information                                                      
34: R23         Allowance for Credit Losses                         HTML     52K 
35: R24         Subsequent Events                                   HTML     39K 
36: R25         Basis of Presentation and Summary of Significant    HTML    176K 
                Accounting Policies (Policies)                                   
37: R26         Basis of Presentation and Summary of Significant    HTML     51K 
                Accounting Policies (Tables)                                     
38: R27         Revenue Recognition (Tables)                        HTML    113K 
39: R28         Net Loss per Share (Tables)                         HTML     35K 
40: R29         Investments in Non-Marketable Securities (Tables)   HTML     40K 
41: R30         Fair Value Measurements (Tables)                    HTML     49K 
42: R31         Balance Sheets Details (Tables)                     HTML     80K 
43: R32         Stock-based Compensation (Tables)                   HTML    175K 
44: R33         Income Taxes (Tables)                               HTML    118K 
45: R34         Commitments and Contingencies (Tables)              HTML     80K 
46: R35         Segment, Geographical and Other Revenue             HTML    164K 
                Information (Tables)                                             
47: R36         Allowance for Credit Losses (Tables)                HTML     53K 
48: R37         Subsequent Events (Tables)                          HTML     45K 
49: R38         Description of Business (Details)                   HTML     58K 
50: R39         Basis of Presentation and Summary of Significant    HTML     74K 
                Accounting Policies - Narrative (Details)                        
51: R40         Basis of Presentation and Summary of Significant    HTML     39K 
                Accounting Policies - Plant, Property, and                       
                Equipment (Details)                                              
52: R41         Revenue Recognition - Disaggregation of Revenue     HTML     61K 
                (Details)                                                        
53: R42         Revenue Recognition - Contracts with Customer       HTML     37K 
                (Details)                                                        
54: R43         Revenue Recognition - Additional Information        HTML     38K 
                (Details)                                                        
55: R44         Revenue Recognition - Revenue Recognized (Details)  HTML     41K 
56: R45         Revenue Recognition - Performance Obligation        HTML     59K 
                (Details)                                                        
57: R46         Net Loss per Share (Details)                        HTML     33K 
58: R47         Collaborative Arrangements - GSK Platform           HTML     41K 
                Technology Transfer, Collaboration and License                   
                Agreement (Details)                                              
59: R48         Collaborative Arrangements - Merck Platform         HTML     40K 
                Technology Transfer and License Agreement                        
                (Details)                                                        
60: R49         Collaborative Arrangements - Merck Sitagliptin      HTML     47K 
                Catalyst Supply Agreement (Details)                              
61: R50         Collaborative Arrangements - Enzyme Supply          HTML     34K 
                Agreement (Details)                                              
62: R51         Collaborative Arrangements - Tate & Lyle (Details)  HTML     45K 
63: R52         Collaborative Arrangements - Nestle Global          HTML     71K 
                Development Agreement (Details)                                  
64: R53         Collaborative Arrangements - Porton (Details)       HTML     56K 
65: R54         Collaborative Arrangements - Novartis (Details)     HTML     49K 
66: R55         Collaborative Arrangements - Roche (Details)        HTML     44K 
67: R56         Collaborative Arrangements - Takeda (Details)       HTML     45K 
68: R57         Collaborative Arrangements - Molecular Associates   HTML     61K 
                Inc (Details)                                                    
69: R58         Collaborative Arrangements - Performance Period     HTML     55K 
                (Details)                                                        
70: R59         Investments in Non-Marketable Securities (Details)  HTML     46K 
71: R60         Fair Value Measurements (Details)                   HTML     53K 
72: R61         Balance Sheets Details - Cash and Cash Equivalents  HTML     41K 
                (Details)                                                        
73: R62         Balance Sheets Details - Schedule of Inventory      HTML     37K 
                Components (Details)                                             
74: R63         Balance Sheets Details - Property and Equipment,    HTML     53K 
                net (Details)                                                    
75: R64         Balance Sheets Details - Goodwill (Details)         HTML     31K 
76: R65         Balance Sheets Details - Accrued Liabilities        HTML     37K 
                (Details)                                                        
77: R66         Stock-based Compensation - Narrative (Details)      HTML    138K 
78: R67         Stock-based Compensation - Stock-Based              HTML     44K 
                Compensation Expense (Details)                                   
79: R68         Stock-based Compensation - Assumptions Used         HTML     48K 
                (Details)                                                        
80: R69         Stock-based Compensation - Option Activity          HTML     79K 
                (Details)                                                        
81: R70         Stock-based Compensation - Award Activity           HTML    106K 
                (Details)                                                        
82: R71         Capital Stock (Details)                             HTML     56K 
83: R72         401(k) Plan (Details)                               HTML     30K 
84: R73         Income Taxes - Components of Loss Before Provision  HTML     38K 
                for Income Taxes (Details)                                       
85: R74         Income Taxes - Components of Provision for Income   HTML     49K 
                Taxes (Details)                                                  
86: R75         Income Taxes - Tax Rate Reconciliation (Details)    HTML     51K 
87: R76         Income Taxes - Components of Deferred Tax Assets    HTML     68K 
                and Liabilities (Details)                                        
88: R77         Income Taxes - Narrative (Details)                  HTML     42K 
89: R78         Income Taxes - NOL Carryforwards and Federal        HTML     40K 
                Research and Development Tax Credits (Details)                   
90: R79         Income Taxes - Reconciliation of Unrecognized Tax   HTML     36K 
                Benefits (Details)                                               
91: R80         Commitments and Contingencies - Narrative           HTML    113K 
                (Details)                                                        
92: R81         Commitments and Contingencies - Lease Costs         HTML     47K 
                (Details)                                                        
93: R82         Commitments and Contingencies - Other Lease         HTML     51K 
                Information (Details)                                            
94: R83         Commitments and Contingencies - Lease Maturity      HTML     48K 
                Under Topic 842 (Details)                                        
95: R84         Commitments and Contingencies - Other Commitments   HTML     36K 
                (Details)                                                        
96: R85         Related Party Transactions (Details)                HTML     63K 
97: R86         Segment, Geographical and Other Revenue             HTML     33K 
                Information - Narrative (Details)                                
98: R87         Segment, Geographical and Other Revenue             HTML     90K 
                Information - Segment Reporting (Details)                        
99: R88         Segment, Geographical and Other Revenue             HTML     48K 
                Information - Concentration Risk (Details)                       
100: R89         Segment, Geographical and Other Revenue             HTML     44K  
                Information - Revenues (Details)                                 
101: R90         Segment, Geographical and Other Revenue             HTML     40K  
                Information - Goodwill (Details)                                 
102: R91         Allowance for Credit Losses - Analysis of           HTML     34K  
                Allowance for Credit Losses (Details)                            
103: R92         Allowance for Credit Losses - Summary of Accounts   HTML     42K  
                Receivable by Aging Category (Details)                           
104: R93         Subsequent Events - Narrative (Details)             HTML     50K  
105: R94         Subsequent Events - Lease Maturity (Details)        HTML     53K  
106: R9999       Uncategorized Items - cdxs-20201231.htm             HTML     31K  
108: XML         IDEA XML File -- Filing Summary                      XML    204K  
11: XML         XBRL Instance -- cdxs-20201231_htm                   XML   3.44M 
107: EXCEL       IDEA Workbook of Financial Reports                  XLSX    168K  
 7: EX-101.CAL  XBRL Calculations -- cdxs-20201231_cal               XML    274K 
 8: EX-101.DEF  XBRL Definitions -- cdxs-20201231_def                XML   1.12M 
 9: EX-101.LAB  XBRL Labels -- cdxs-20201231_lab                     XML   2.17M 
10: EX-101.PRE  XBRL Presentations -- cdxs-20201231_pre              XML   1.53M 
 6: EX-101.SCH  XBRL Schema -- cdxs-20201231                         XSD    217K 
109: JSON        XBRL Instance as JSON Data -- MetaLinks              501±   736K  
110: ZIP         XBRL Zipped Folder -- 0001200375-21-000021-xbrl      Zip    693K  


‘EX-101.CAL’   —   XBRL Calculations — cdxs-20201231_cal


This Exhibit is an XBRL XML File.


                                                                                                                                                                                
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<!-- XBRL Document Created with Wdesk from Workiva -->
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2 Subsequent Filings that Reference this Filing

  As Of               Filer                 Filing    For·On·As Docs:Size             Issuer                      Filing Agent

 5/07/21  Codexis, Inc.                     424B5                  1:401K                                   Donnelley … Solutions/FA
 5/07/21  Codexis, Inc.                     S-3ASR      5/07/21    4:636K                                   Donnelley … Solutions/FA


32 Previous Filings that this Filing References

  As Of               Filer                 Filing    For·On·As Docs:Size             Issuer                      Filing Agent

11/06/20  Codexis, Inc.                     10-Q        9/30/20   98:9.7M
 5/08/20  Codexis, Inc.                     10-Q        3/31/20   80:8.5M
 2/28/20  Codexis, Inc.                     10-K       12/31/19  101:17M
11/06/19  Codexis, Inc.                     10-Q        9/30/19   82:10M
 8/06/19  Codexis, Inc.                     10-Q        6/30/19   77:10M
 6/21/19  Codexis, Inc.                     S-8         6/21/19    9:454K                                   Donnelley … Solutions/FA
 5/08/19  Codexis, Inc.                     10-Q        3/31/19   80:7.6M
 3/01/19  Codexis, Inc.                     10-K       12/31/18  102:13M
11/09/18  Codexis, Inc.                     10-Q        9/30/18   74:11M
 8/09/18  Codexis, Inc.                     10-Q        6/30/18   72:9.5M
 3/15/18  Codexis, Inc.                     10-K       12/31/17   89:10M
11/09/17  Codexis, Inc.                     10-Q        9/30/17   68:6.7M
 8/09/17  Codexis, Inc.                     10-Q        6/30/17   66:7M
11/08/16  Codexis, Inc.                     10-Q        9/30/16   65:5.7M
 8/09/16  Codexis, Inc.                     10-Q        6/30/16   62:5.3M
 3/08/16  Codexis, Inc.                     10-K       12/31/15   89:8.3M
11/06/15  Codexis, Inc.                     10-Q        9/30/15   64:7.6M
 5/07/15  Codexis, Inc.                     10-Q        3/31/15   65:5.5M
11/06/14  Codexis, Inc.                     10-Q        9/30/14   76:9.6M
11/12/13  Codexis, Inc.                     10-Q        9/30/13   70:6.4M
 4/02/13  Codexis, Inc.                     10-K       12/31/12   94:15M                                    Workiva Inc.
11/07/12  Codexis, Inc.                     10-Q        9/30/12   68:5.1M                                   Donnelley … Solutions/FA
 9/04/12  Codexis, Inc.                     8-K:1,2,3,5 8/28/12    5:380K                                   Donnelley … Solutions/FA
 8/09/12  Codexis, Inc.                     10-Q        6/30/12    9:1.1M                                   Donnelley … Solutions/FA
 5/10/12  Codexis, Inc.                     10-Q        3/31/12   33:2.2M                                   Donnelley … Solutions/FA
 8/03/11  Codexis, Inc.                     10-Q        6/30/11   29:2.5M                                   Donnelley … Solutions/FA
 5/06/11  Codexis, Inc.                     10-Q        3/31/11    5:927K                                   Donnelley … Solutions/FA
11/04/10  Codexis, Inc.                     10-Q        9/30/10    5:820K                                   Donnelley … Solutions/FA
10/28/10  Codexis, Inc.                     8-K:1,2,9  10/28/10    4:463K                                   Donnelley … Solutions/FA
 5/28/10  Codexis, Inc.                     10-Q        3/31/10    6:850K                                   Donnelley … Solutions/FA
 3/31/10  Codexis, Inc.                     S-1/A                  9:3.7M                                   Donnelley … Solutions/FA
12/28/09  Codexis, Inc.                     S-1                   37:5.9M                                   Donnelley … Solutions/FA
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