LabJ User`s Manual
Contents
1. LabJ License and Usage Conditions The LabJ by anybody purpose Neverthe your loc add a val is usable for any commercial but al less you it feat may adap needs and redistribute copies ol uable che for is not yet complet the functio chemistry community non commercial free o or purely ely nali of the ure or hunt down a contact cer th e autho tainly integrated in However the LabJ program package Formation Sys a LabJ package as a par in providing the LabJ as in must be negotia nf The or LabJ S tm Inc Ml n requires Draw and DL y agreemen iated com S pa endorse LabJ ply any s Linux is registere uc d a mark o DL author ass for damages resulting from M nies are in nor does h associatio tems ted umes package ca Partic r by email and the to the of ficial CY the package you are we feature will release of LabJ bug fix or t be dis ularly the auth and its aff no ju TAC or strictly forbid of any produc tegrated pa liated companies to f anybody is in CETO for errors or malf tributed as part of charge in house true GPL GNU prog2. REF 24 25 OK NOTE Acc to TLC during CC conversion is near 90 100 only traces of A are detected e Quant D pton Anal Data Identification 0328 Z C26H4204Si 446 71 viscous colorless oil a 20 D 188 2 0 78 CHCI3 o Chiral TLC NMR MS HRMS IR 3S 11aR 14R 14aR 14 1 tert butyl 1 1 dimethylsilyl oxy 3 pentyl 9 10 didehydro 6 7 8 11 11a 13 14 14a octahydro 3H cyclopenta e oxacyclotri decine 5 12 dione S B and CHCI2 dry 2 mL in toluene dry 10 mL c 1 0 01M was stirred at 80 C t o 85 for 5 hr under argon atmosphere Then the mixture was evaporated and the residue was subjected to the CC EH 7 5 PROCEDURE Th Weight Pract Amt g Volume density Molarity Purity em Eme SESS Zee orimt mL o P999 mu tum moti pal TNT A CaoH4gO4Si 500 80 1 000 0 000100000 0 10000 50 08 0 05280 7 1 054 100 GRL GA 039 02 B CagH54MoNs 624 79 0 075 0 000100000 0 00750 4 69 0 00500 7 1 066 100 1 omd 4douco o dOCOODu 446 71 1 054 0 0001000000 0 10540 47 08 0 0328 B 0 073426 n
3. Chiral i PRMe CH2CI2 c A 0 01M 16h 80 C REF 24 25 Sketch OK NOTE Acc to TLC during CC conversion is near 90 100 only traces of A are detected Descripton Anal Data Identification 0328 fr 32 56 1 TLC NUR CogH42048i 446 71 viscous colorless oil a 20 D 188 2 0 78 CHCI3 3S 11aR 14R 14aR 14 1 tert butyl 1 1 dimethylsilyl oxy 3 pentyl 9 10 didehydro 6 7 8 11 11a 13 14 14a octahydro 3H cyclopentafe oxacyclotri decine 5 12 dione A mixture of A B and CHCI2 dry 2 mL in toluene dry 10 mL c 1 0 01M was stirred at 80 C t o 85 for 5 hr under argon atmosphere Then the mixture was evaporated and the residue was subjected to the CC EH 7 5 PROCEDURE Th ur Pract Amt g Volume density Molarity Purity em rw rat eee eee glorimt mL o ym morti rd C39H4gO4Si 500 8d 1 000 0 000100000 0 10000 50 7 0 05280 1 1 054 100 GRL GA 039 02 CagHs4MoN3 624 79 0 075 0 000100000 0 00750 4 69 0 00500 7 1 066 100 ee er Th Yield mmol Th Yield mg P Yield g Purity 24 P Yield mmol P Yield ed o dOCOODv CogH42048i 446 71 1 054 cd 0 10540 47 08 0 0328 0 073426 m KEYWORDS ID C26H4204Si PGE2LA RCM Mo chiral 41 LabJournal v 2 3 0 c K Grela 1996 1999 Data Browse Form mmols Max Planck Institut f r Kohlenforschung REACTION Chiral i PhMe CH2CI2 c A 0 01M 16h 80 C
4. ELN stores chemical information and assists in planning chemical reactions It calculates information such as molecular weights moles reactant amounts and volumes percent yields and more Notes procedures results references comments graphics etc can be attached to the LabJ records LabJ can be also used to store various data of synthesized compounds such as melting and boiling points spectral data as well as unlimited number of custom fields for your specific needs LabJ is realized as a database file labj db for MDL ISIS Base program Reaction drawings and sub structure searches use the ISIS Draw module Following is a brief overview of the most prominent features of LabJ LabJ is a calculations and database program a k a electronic laboratory notebook ELN for organic chemists It can be used e g in classical organic synthesis incl total synthesis screening for catalysts optimization etc parallel and automated synthesis solid support synthesis Chemical reactions can be easily introduced graphically by drawing them in ISIS Draw module LabJ eliminates most of the tedious work of calculating chemical reaction data such as molecular formulas and weights of reactants and products amounts and volumes of the reactants and yields of products Calculations are based on graphical reaction and choosed scale stoichi ometry and purity of reagents Volumes of reactants are calculated based on
5. Optional To remove all data from the form choose Edit gt Clear Data gt Form Select the REACTION box if not highlighted Do one of the following Draw a new query Import a query from a rxnfile Restore a query that you previously saved as an object in the database see Help ISIS Base Search Types for details page 12 To draw a new query Transfer to ISIS Draw Select the REACTION box Click the ISIS Draw Transfer icon at the top of the ISIS Base toolbar to start ISIS Draw Alternatively you can double click inside the REACTION box Draw the query in ISIS Draw Hint To learn how to speed up drawing process consult Help gt ISIS Draw Contents gt QUICK START See page 12 for details m Click the ISIS Base Transfer icon at the top of the ISIS Draw toolbar to transfer the molecule into the reaction box in the ISIS Base form Choose Search gt Current Rxn Page 13 Karol Grela LabJ Electronic Laboratory Notebook m Click the Browse mode if not highlighted You see the first record displayed on the boxes and tables in your form To see how many records you retrieved click the REACTION box if not selected and check the status bar Use and gt buttons to display the record that you want to view This search tool generates a list that can be saved browsed i printed as separated pages or in tabular form or exported as o C a ne
6. either reagents density or molarity M mol L Because LabJ uses ISIS Base program as a database engine all records can be easily stored and searched If you want to re examine or scale up a reaction simply retrieve an existing record duplicate it change one or more values incl reagents and everything is recalcu lated All records in a LabJ database are sequenced in numeric order based on reaction number e g KG 1023 Simillary all products and fractions can be logically labelled based on reaction number e g KG 1023 1 3 m You can browse through the database page by page or Page 1 Karol Grela Bugs Copyright Installation System Requirements Download LabJ Electronic Laboratory Notebook search for a record by reaction number reaction scheme sub structure analytical data procedure keywords and much more This search tool generates a list that can be browsed printed as separated pages or in tabular form or saved as a new LabJ database LabJ prints records in a form of Reaction Page Report Page Tabular Form and various Analytical Forms e g for IR NMR and MS departments as well as virtually unlimited number of custom forms for your specific needs LabJ was originally written for my own use and a lot of it is messy so ideas on how to clean it up would be great You are welcome to read the database structure source code of LabJ and to try to modify it and save as your ow
7. first big yellow table called SUBSTRATES Figure 1 m Click the first cell in the column called RATIO Type 1 in the first cell of the RATIO column Enter 1 and 1 2 in the second and third cell in this column In this example you calculate the reaction in a scale of mmol Click the first cell in the column called SCALE Type 0 001 in the first cell of the SCALE column Usually the values used in this column are the same for all substrates and products and are equal to the scale of the reaction Therefore type 0 001 in the second and third cell in this column Page 5 Karol Grela LabJ Electronic Laboratory Notebook KEYWORDS ID DATE PGE2 104 GRL GA LabJournal v 2 3 1 c K Grela 1996 2000 Data Input Form MMOLS Electronic Laboratory Notebook S U B S T R A T E S igure 1 Hint To speed up typing you can use Edit gt Copy and Paste from the menu or Ctrl C Ctrl V from the keyboard Select the spreadsheet connected to the stoichiometry of the products It is the second yellow table called PRODUCTS Figure 1 m Click the first cell in the column called RATIO Type EM Select the first cell in the column called SCALE Type 0 001 Choose Database gt End Update to update the new data into the LabJ You will see amounts of reagents and product s in the QUANT calculated amounts in millimols TH WEIGHT calculated amounts
8. in milligrams and TH YIELD yield of theory columns Figure 2 Page 6 Karol Grela LabJ Electronic Laboratory Notebook piu earn igure 2 Calculating amounts of the reagents incl reagents volumes Select the SUBSTRATES table Click the second cell in the column called PURITY In this example the NaH is used as a 40 wt suspension in mineral oil Therefore type 40 in this cell m Click the third cell in the column called DENSITY Type 1 3968 the density of allyl bromide Choose Database gt End Update to update the new data into the LabJ You will see new weight of NaH suspension in the TH WEIGHT cell and a volume in mL of allylbromide in the VOLUME cell Figure 3 m Review all of the data for the DATA INPUT form and correct any mistakes To correct mistakes click in the box that contains the error double click in case of the REACTION box Executing the reaction Weigh out the reagents and start the reaction In the event you use different amounts of reagents than you calculated before you should input the real amounts of reagents used Page 7 Karol Grela S U B S q R A T E S LabJ Electronic Laboratory Notebook Select the SUBSTRATES table Click the cell in the column called PRACT AMT In this example type 0 175 in the first cell That means that you have used exactly the calculated amount of phenol Cli
9. 4204Si PGE2LA RCM Mo chiral 41 GRL GA 041 LabJournal v 2 3 0 c K Grela 1996 2000 Data Input Form MMOLS Max Planck Institut f r Kohlenforschung REACTION Chemist and Reaction Code user s input Chiral Chiral Formula and Molecular Weight generated Reagent Number user s input Formula Ratio Scale mol Quant mmol Th Wei Pract g Excess Volume densi Molarity Purity enn g or mL mL mL g mL mol L A CaoHa4gO4Si 500 80 1 000 0 000100000 0 10000 50 08 0 05280 7 1 054 B CggHs4MoNg 624 79 0 075 0 000100000 0 00750 4 69 0 00500 7 1 066 Scale of Reaction a of Reagent user s input calculated M SEEN a En a io Fond adi ne Tes E 446 71 0 0001000000 0 10540 47 08 0 0328 073426 Ratio of Products Eua of ues io and Molecular E L oA s input Eua s input NJ ME Weight generated Theorethical Amount of Product calculated Experimental Description of Reaction user s input OmArDAHDCH Volume of Reagent based on density or molarity M ae aoco PROCEDURE 1 TLC NMR Cf Browse Form for this fields REF 24 25 OK Anal Data Appendix 2 KEYWORDS ID C26H4204Si PGE2LA RCM Mo chiral GRL GA 041 LabJournal v 2 3 0 c K Grela 1996 1999 Data Browse Form mmols Max Planck Institut f r Kohlenforschung REACTION
10. CTURE Structure 33 fmla MOLSTRUCTURE Formula 34 mol weight MOLSTRUCTURE Real 35 CORP ID 20 Fixed Text 36 PROD EQ Real 3d PROD nT Real 38 PROD mT Real 39 PROD mP Real 40 PROD nP Real 41 PROD YIELD Real 42 PROD DESC Variable Text 43 REF PRODUCT Real Page 18 Karol Grela LabJ Electronic Laboratory Notebook 44 PROD_PP Real 64 PROD_ANAL Variable Text 77 PROD_NAME Variable Text 45 DATE 10 Fixed Text 46 GDH Integer 47 PROC Variable Text 48 ANAL Parent 49 FRACTION_NO Variable Text 74 FRACTION_DESCR Variable Text 75 FRACTION_QUANT Variable Text 76 FRACTION_ANAL Variable Text 54 RESULTS Variable Text 55 RXNCOND Variable Text 56 RXNCOND Variable Text 57 RESULTS SKETCH Sketch 58 KEYWORDS Variable Text 61 YIELD 10 Fixed Text 78 NAME O07 Fixed Text Page 19 Appendix 1 KEYWORDS ID DATE C26H4204Si PGE2LA RCM Mo chiral 1999 09 29 ACEC GO LabJournal v 2 3 0 c K Grela 1996 2000 Data Input Form MMOLS Max Planck Institut f r Kohlenforschung REACTION Chiral omad ma4ouco Q dOoCOODUv A mixture of A B and CHCI2 dry 2 mL in toluene dry 10 mL c 1 0 01M was stirred at 80 C t o 85 for 5 hr under argon atmosphere Then the mixture was evaporated and the residue was subjected to the CC EH 7 5 PROCEDURE Descripton Anal Data Identification fr 32 56 1 TLC NMR Anal Data KEYWORDS ID C26H
11. actions samples To describe different fractions obtained during product isolation and purification you can fill a special table You can also use this table to track sample flow Figure 6 Select the box that is connected to the FRACTIONS field It is the large table on the bottom called FR cf APPENDIX A and B Choose Edit gt New Record ISIS Base creates a new sub record row that appears in the FR table Select the newly created row in this table and type fraction number and weight fraction description etc Repeat above steps for each sample fraction Choose Database gt End Update to register the new record Figure 6 Page 9 Karol Grela LabJ Electronic Laboratory Notebook pda ii opo deccm Ex Tj e eeu igure 5 Hint You can delete a existing row in the FR table Click the row you want to delete m Choose Edit gt Delete Record ISIS Base deletes one sub record row Choose Database gt End Update to update changes Inserting additional data In the sample forms used in the LabJ notebook each form box has a label that describes the type of data to enter To enter additional data chemist s and experiment code keywords date conditions and notes see APPENDIX A and B Registering the record into the LabJ database When you complete the data entry for one reaction you can finally register the record into the database Choose Database gt End U
12. ahead aie Ria ee Page 1 BUS x e aaen ertet e dot Gus e totl Ga da R db RE dabo er aub abe adv ala d a d eres Page 2 Copytiglit us gi ione babes pa em ated aa RIS o DEG Ld mu ae eee uei koi Page 2 Installation aai emea cLc Page 2 System Requirements aaa Page 2 Download 2er RERBA PoeeheG Sep Sep EEG ee PS vee ES Page 2 Installation sos sce rep Grate Ae Beate he Reus edis Ge Os ae made do tn Page 3 Wsing aby sis kane ee alee BMS wee we eS eS ae WN Dee SO Deg Sd ae deg ce Page 3 A Brief Lesson 20 ee eee Page 3 Registration of Reaction 2 0 cee nn Page 4 Opening the LabJ database n n aaaea ee Page 4 Creating a new record 2 0c ee Page 4 Entering a reaction onto the form llle Page 5 Calculating stoichiometry of the reaction 00000 eee eee Page 5 Calculating amounts of the reagents incl reagents volumes Page 7 Executing the reaction 0 2 0 ee ee Page 7 Finishing the reaction 00 00 ce ee Page 8 Calculating the yield of product s incl product purity Page 9 Tracking the fractions samples llle Page 9 Inserting additional data aaea Page 10 Registering the record into the LabJ database 0045 Page 10 Advanced 230 addere gebe Runs mi Se que RU Sor d UR Rupe S RR ce aee Sar dn xd Page 11 Logging Database Transactions 0 cece es Page 11 Data tyDe6S s ues uce s
13. ck the second cell in the column called PRACT AMT Type 0 0650 you have added a slight excess of sodium hydride Click the third cell in the column called PRACT AMT Type 0 1 allylbromide was added neat by a micro syringe Because the value of 0 1 corresponds to the volume of allylbromide you have to change the number in the next column from 1 to 0 12g O2mL Choose Database End Update to update the new data into the LabJ You will see the calculated excess of the reagents in the EXCESS column Figure 4 Finishing the reaction Select the box connected to the description of of the reaction It is the big box called PROCEDURE AP PENDIX A Note the reaction conditions additions of reagents temperature etc Describe the work up proce dure and the isolation and purification of product s Choose Database End Update to update the new data into the LabJ Page 8 Karol Grela basilica ean el ub cid rj igure 4 LabJ Electronic Laboratory Notebook Calculating the yield of product s incl product purity Select the PRODUCTS table Click the cell in the P YIELD column In this exam ple the yield of an analytically pure product is 198 mg Therefore type 0 198 in this cell Choose Database gt End Update to calculate the yield You will see the yield of product calculated as mmols and of theory in the P YIELD cells Figure 5 Tracking the fr
14. e To see a complete list of all the searches that you can do in ISIS Base see Help ISIS Base Search Types Editing a record m Click the Update button To change a data click in the box that contains the data double click in case of the REACTION box See chapter Registration of Reaction page 4 for more information Choose Database gt End Update to update the new record Deleting a record Caution Make a backup of your LabJ database before you begin Click the Update button Select the REACTION box Choose Edit Delete Record ISIS Base deletes one record of your LabJ notebook Editing a reaction manually When you draw a reaction LabJ automatically registers all substrates and products into the appropriate tables You can also manually add or delete a reagent in the SUBSTRATES spreadsheet Similarly you can manually add or delete products in the PRODUCTS spreadsheet You will see changes only in SUBSTRATES or PRODUCTS tables but not in the REACTION box Caution Make a backup of your LabJ database before you begin Page 15 Karol Grela Modifying LabJ LabJ Electronic Laboratory Notebook To add a new reagent or product m Select the row after which you want to add a new sub record in the SUBSTRATES or PRODUCTS spread sheet Choose Edit gt New Record ISIS Base creates a new sub record row that appears in the table Select the
15. eaction use default form DATA INPUT MMOLS for reactions of scale 0 1 mol or open a form called DATA INPUT MOLS if reaction scale 20 1 mol See page 3 for how to open forms Page 4 Karol Grela LabJ Electronic Laboratory Notebook Entering a reaction onto the form In this example you will calculate the reaction between one equivalent of phenol and one equivalent of NaH and a slight excess of allyl bromide 1 1 1 2 producing one equivalent of corresponding ether in a scale of 1 mmol To enter the reaction onto the form Select the box that is connected to the reaction field It is the large box on the top called REACTION Figure 1 m Click the ISIS Draw Transfer icon at the top of the ISIS Base toolbar to start ISIS Draw Alternatively you can double click inside the REACTION box Draw the reaction scheme in ISIS Draw Hint To learn how to speed up drawing process consult Help ISIS Draw Contents QUICK START See page 12 for details m Click the ISIS Base Transfer icon at the top of the ISIS Draw toolbar to transfer the reaction into the structure box in the ISIS Base form Choose Database gt End Update to register the new record You will see a reaction scheme and reagents formulas and formula weights in the ISIS Base window Figure 1 Calculating stoichiometry of the reaction Select the spreadsheet that is connected to the stoichi ometry of the reagents It is the
16. lose the database To do so choose File gt Close Database Choose File gt Configure Database The File Open dialog box appears Double click the name labj db Mac labj Page 11 Karol Grela Getting Help LabJ Electronic Laboratory Notebook Ensure that the Log database transactions setting is On Click OK Backup and delete the transaction log file after you view or print the transactions Each time that you register data for the database information is appended to the end of the file and it can quickly increase in file size Note Data types Each field in the LabJ database has restrictions on the type of data it stores If you enter the wrong type of data for a field a warning message appears For example if you enter text for a field that expects a number you see the message Error in data format a n Real value was expected To view the database fields and their field types choose Database View Definition Note Formula and Molecular Weight LabJ automatically calculates data for the FORMULA and Formula Weight FW boxes when you register the reaction For future reference you can enter a molecular weight instead of having the program calculate it for you but you cannot enter a formula The ISIS Desktop online help has detailed examples and step by step instructions to help you complete your tasks in the LabJ program To use the ISIS Desktop online help To acce
17. n LabJ Database Please send bug descriptions suggestions new LabJ files or successful stories to grela technologist com cf Copyright This program is free software you can redistribute it and or modify it under the terms of the GNU General Public License as published by the Free Software Foundation either version 2 of the License or at your option any later version This program is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY without even the implied warranty of MERCHANT ABILITY or FITNESS FOR A PARTICULAR PURPOSE See the GNU General Public License for more details You should have received a copy of the GNU General Public License along with this program if not write to the Free Software Foundation Inc 59 Temple Place Suite 330 Boston MA 02111 1307 USA For using LabJ program the ISIS Desktop ISIS Base and ISIS Draw software package is needed Please contact MDL Information Systems Inc for more information Currently you can use LabJ with ISIS Base 1 x and 2 x recommended for Microsoft Windows 3 x 95 98 2000 and NT Apple Macintosh and IRIX SGI It is also possible to use LabJ under Linux with Microsoft Windows emulator such as WABI and Win4Lin M The newest version of the package can be downloaded from http zinc ichf edu pl labj Page 2 Karol Grela Installation Using LabJ A Brief Lesson LabJ Electronic Laboratory Notebook u Get labjlx zi
18. n Undo many of the changes that you make when you edit a form Caution Make a backup of your LabJ database before you begin Click the Forms button Do one of the following Optional create display new box create a new table or create a new column in an existing table Optional change the field that is connected to a box or column Optional edit one of the following Boxes or Columns or Tables Box labels or column headings Chemical display of structures Text or numeric data display Lines or Text Entire form Do one of the following To save a new form or an existing form under the same name choose File gt Save Form For new forms only enter a name and an optional description for the form To save an existing form under a new name choose File gt Save Form As Enter a name and an optional description for the form m Click OK The form is saved inside the database and you will not see it as a separate form file on disk Example In this example you will change the default chemist s code e g GRL GA Figure 7 Use this procedure to set a default string for this code Click the Forms button Select a box that is connected to a chemist s code field Name It is a blue box on the right top of the default form see APPENDIX A and B Choose Object Box Properties and then click the Function tab Page 17 Karol Grela Anatomy of LabJ LabJ Electronic Lab
19. newly created row and type a Formula Weight but not a Formula ratio scale etc See chapter Registration of Reaction page 4 for more information Choose Database gt End Update to update the new record To delete an existing reagent or product Click the row you want to delete in the SUBSTRATES or PRODUCTS spreadsheet Choose Edit gt Delete Record ISIS Base deletes one sub record row Choose Database gt End Update to update changes Hint You can also add or delete rows in the FR table See chapter Registration of Reaction page 4 for more information Updating the changed record into the LabJ When you complete data entry for one reaction you can update the record into the database Choose Database gt End Update m Optional to close the database choose File gt Close Database LabJ can display or print records in a form of Reaction Page Report Page Tabular Form and various Analytical Forms e g for IR NMR and MS departments as well as virtually unlimited number of custom forms for your specific needs To learn how to create or edit forms to view search results or to enter data into a database choose Help ISIS Base Contents Creating and Editing FORMS Page 16 Karol Grela LabJ Electronic Laboratory Notebook Creating and Editing Forms GRL GA 104 Figure 7 This procedure will show you how to create or edit a form Hint You ca
20. of an appropriate form for data entry Page 3 Karol Grela Registration of Reac tion Update LabJ Electronic Laboratory Notebook Optional To make this form the default form you see when you open the current database click Set Default Form Click OK You see the selected form in the window This chapter shows you how to register new records or edit existing records in the laboratory notebook To register a new reaction or changes to an existing record in a LabJ database you typically complete the following steps in the order shown Hint Regularly make backups of your LabJ database Opening the LabJ database Start ISIS Base Open the LabJ database Choose File Open Database Click labj db Mac labj The database opens You see the default data entry form in the LabJ database win dow Choose Search gt Retrieve All to retrieve all existing records Use button to display the last record Creating a new record Before you enter data onto a form you must create a new record Click the Update button Choose Edit gt New Record ISIS Base assigns a new record number that appears in the ID box cf Figure 1 The ID Number is a unique number that ISIS Base automatically assigns when it creates a new record You can change the ID number before the record is regis tered but not after For LabJ typical use do not change the default ID number According to the scale of the planned r
21. oratory Notebook Click the Default data box and choose String Type a new chemist s code e g PRR PA Click OK Choose File Save Form You are welcome to read the database structure source code of LabJ and to try to modify it and save as your own LabJ Database To find out more about the ISIS Base features choose Help ISIS Desktop Contents ISIS Overview and Docu mentation Table 1 The LabJ database structure O0 RXN Parent 1 RXNREGNO Integer 2 RXNSTRUCTURE Reaction 3 VARIATION Parent 4 VARIATION_NO Integer 5 REACTAN Parent 6 REACTANT_NO Integer 7 LIST_OF_REACTANTS Integer 8 PRODUCT Parent 9 PRODUCT_NO Integer 10 LIST_OF_PRODUCTS Integer 11 REACTANT LINK Parent 12 LIST OF REACTANTS Integer 13 REACTANT NO Integer 14 OL Parent 15 REF REAGNT Real 16 OLREGNO Integer 17 OLSTRUCTURE Structure 18 fmla MOLSTRUCTURE Formula 19 mol weight MOLSTRUCTURE Real 20 CORP ID 20 Fixed Text 21 REACT EQ Real 22 REACT n Real 23 REACT m Real 24 REACT V Real 25 REACT d Real 26 REACT P Real 59 REACT DESC 64 Fixed Text 60 REACT Molarity Real 62 REACT mP Real 63 REACT Exs Real 79 REACT Exs Unit Integer 27 PRODUCT LINK Parent 28 LIST OF PRODUCTS Integer 29 PRODUCT NO Integer 30 MOL Parent 31 OLREGNO Integer 32 OLSTRU
22. p for ISIS Base 1 x or labj2x zip for ISIS Base 2 x from http zinc ichf edu pl labj u Use unzip zip command DOS to extract the labj db file from the archive Alternatively you can use any GUI program like WinZip Windows to extract the archive file Start ISIS Base program and open the abj db file This chapter explains how to use LabJ on your computer Opening the abj db file Retrieving existing records Browsing records Retrieving forms Use this procedure to open LabJ Start ISIS Base Choose File gt Open Database Change to the directory Mac folder where the labj db file is located Click the name of the abj db Mac labj file to open Click OK Mac Open You will see a default form in the ISIS Base window A form is required for searching or to register data in the database In LabJ electronic notebook a form called DATA INPUT MMOLS is used as a default form Consult APPENDIX A for a detailed description of fields in DATA INPUT form Choose Search gt Retrieve All to retrieve all existing records LabJ database contains five sample reactions Click the 9 buttons or use Up and Down cursor keys to move between records For browsing and printing records a separate form is provided called DATA BROWSE Consult APPENDIX B for a detailed description of fields in DATA BROWSE form To retrieve a form Choose File gt Open Form Click the name
23. pdate The data is registered as a new record that can be retrieved in a search m Optional to close the database choose File gt Close Database Page 10 Karol Grela Figure 6 Advanced LabJ Electronic Laboratory Notebook Descripton Anal Data Identification Fractions 22 29 in column chrom hexan EtOAc 9 1 Pure product TLC NMR MS GRL GA 104 01 gt to Sample Repository of MPI GRL GA 104 01 gt to Bayer GmbH Wuppertal bio Caution Make a backup of your LabJ database before you begin Hint Logging Database Transactions Activate the database journal to log transactions for a database during registration When you register new records during data entry ISIS Base creates the log file using the name of the database with a og file extension The log file is saved in the same directory Mac folder as the database Each transaction is added to the end of the log file until you delete the file View or print the log file using a word processor The ISIS Base transaction log records database transactions that occur during registration The log is a text ASCII file that you can view or print later The log file records Registration of new records Updating of existing records Deletion of existing records Date and time each operation occurred Use this procedure to instruct ISIS Base to log database transactions that occur during registration for the LabJ database Ifthe LabJ database is open c
24. ram program to you lcome be anot the incl to most M er DL de teres f another package unctio ed is t no responsibility from the use se oj prop of the programs rietary software S S tm Base from which DL regis Infor available unde http www md O way associat your use of S are from S programs M T DL Information the appropriate Systems licensing li com MDL and its af Fil ed with nor do any of S S S Draw and or n or endorsemen tered trademark of trademark in the United Sta M mation Systems Inc are c M DL In formati ion Systems Inc Karol Grela Ph grela icho edu pl D Base them im Linus Torvalds Boy and ISIS is a M DL is a trade SIS Draw and S S Base All Righ ts Reserved User s Manual Electronic Laboratory Notebook Karol Gre a grela technologist com Institute of Organ OE P ademy of Scie Created Tuesday July 11 2000 for LabJ v 2 3 1 from manual043 wpd using ps2pdf13 v 6 01 for Linux Page i Table of Contents IN OCUCHION PEDE CT Page 1 Description uere eh us Pare us Pathe aia
25. s ADR S UR ee ge le Mle Mle ae wale ake Page 12 Formula and Molecular Weight llle Page 12 Getting Help ae heeded ete k e Reel x RAT EXER AU X e X e dx Ce ded Page 12 To use the ISIS Desktop online help llli Page 12 To learn how to draw llle ren Page 12 To learn how to search 0 0000 es Page 12 To learn about creating and editing forms llli Page 12 To find out more about ISIS applications illii Page 13 Searching Eab ordeo een inate baad eet Re RU ches e seme Peed ed Page 13 Editing Existing Records llle ne Page 14 Locating a record to change 2 ee ees Page 14 Editing areto sss ose RERO ERR ee doceas beg wa aad Page 15 Deleting a record lllllleleee es Page 15 Editing a reaction manually een Page 15 Updating the changed record into the LabJ 2 000 aee Page 16 Modityirig EabJ 24 2 cacacreeaad ao a4 eRSULERSEAUEdE s Adda pg PL MC ES Page 16 Creating and Editing Forms aaaea es Page 17 Anatoimy of babd 22e derent Re Dee RUE PR eR Rc px Rp m ad d Page 18 Appendix A uu ces e ea en Bada Rod er geb hale ached aie ache a t Rb PA debct ede ga Aene Page 20 Appendix B ism m aed ee Aid ee Aad ee e EUER Ger UELLE TR ED TRUE a e Ronda de Page 22 Page ii Page iii Karol Grela Se Introduction Description LabJ Electronic Laboratory Notebook LabJ Laboratory Journal electronic laboratory notebook
26. ss Help choose Help ISIS Desktop Contents Then choose How to Use ISIS Desktop Help This gives you full details on using the ISIS Desktop online help To learn how to draw To quickly learn how to draw structures reactions objects and text for use as search queries records in a database or to insert in a docu ment see Help ISIS Draw Contents QUICK START To learn how to search To see a complete list of all the searches that you can do in ISIS Base see Help ISIS Base Search Types To learn about creating and editing forms To learn how to create or edit forms to view search results or to enter data into a form to register as new records in a database choose Help ISIS Base Contents Creating and Editing FORMS Page 12 Karol Grela Searching LabJ LabJ Electronic Laboratory Notebook u To find out more about ISIS applications To find out more about the following ISIS applications File format conversion ISIS Reaction Database Access System SAR Table or the Add in Manager choose Help gt ISIS Desktop Contents gt ISIS Overview and Docu mentation With LabJ you can search for a record by reaction number reaction scheme sub structure analytical data procedure keywords and much more To see a complete list of all the searches that you can do in ISIS Base see Help gt ISIS Base Search Types Example searching by reaction structure Click the Query button if not highlighted
27. w LabJ database O Click the Browse mode if not highlighted sample query Choose List gt Save Click the List Name box and enter a name for the list without a file name extension Optional To save the query with the same name as the list name you require this setting Save query under the same name Doone ofthe following To store the list as a permanent database object you require this setting amp Permanent E To delete the list when you close the database you require this setting O Permanent sample query a Click OK Editing Existing Re This chapter shows you how to edit or delete existing records cords in the LabJ laboratory notebook To change an existing record in a LabJ database you typically complete the following steps in the order shown Hint Regularly make backups of your LabJ database Locating a record to change Start ISIS Base Open the LabJ database Choose File gt Open Database Click labj db Mac labj The database opens You see the default data entry form in the LabJ database win dow Page 14 Karol Grela Ie gt gt I LabJ Electronic Laboratory Notebook Do one of the following Optional choose Search gt Retrieve All to retrieve all existing records and then select a record you want to change using navigation bar Optional search for records to change by a specific reaction sub structure keywords etc see page 13 for referenc
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