ELN Manual - LabCollector
Contents
1. OVERVIEW 3 OVERVIEW Eus main interface is composed of A menu bar with 5 tabs Home New Book Project Add Log Entry Options ADMIN A search menu by keyword or tag with filters Book Experiment and date A Tree View to switch easily between books experiments and pages A viewer to display books experiments and pages details Find Find Next Find Prev B Generalities 2015 10 08 Description f Edit I DURESS SITE BIOFILM SAMPLING 2 im TRASH 2015 10 08 a Users having access collaborating Note a language selector is integrated to switch easily between English French German and Portuguese interfaces see chapter 3 2 3 1 Admin Menu Only users with an administrator profile can access to the Admin Menu in its entirety New Book Project Add Log Entry Options ADMIN Workflow i E Template Cj Log L Page X Manage OVERVIEW From this menu workflows pages chemical reactions spreadsheet templates and custom fields can be managed to standardize and harmonize writing procedures of experiments see chapter 5 Managers can get an overview on the ELN activity using the Log Activity last 50 entries the audit tools and the task time reports Filters by user and or date range are available to execute more specific audits For more details see chapter 6 Administrators can manage digital certificates pages validation and signing from this menu For more details on these2. A m n m gt o LIE User login K daa a LI daa LI ga E Legende All All Permissions C EW Create Edit Worfklow C ET Create Edit Template ANB Add New Book V AB View All Books 3 1 2 File upload options Administrators can manage file uploads page associated files options OVERVIEW re File Uploads Information PHP max upload size 150M MySQL max allowed packet 100M Configuration Activate Deactivate FileSystem Storage Option Son OorF Max file size authorized in database e 50M Path where files will be stored C Users AgileBio Documents ALS admin labo_virtuel El Legend Not Tested Correct Path Path error Sizes limits per file are defined in the information section You can activate or not this option If this option is not activated files will be registered in the database by default If this option is activated files will be registered in a defined folder Folder has to be defined in the path section To verify your path you can test it Try button legend not tested correct path incorrect path You can also customize the maximum size file 0 to 100M authorized in database 0M Files will be stored in the defined folder path section 100M Files will be stored in the database In the other cases like in the example 1 Files will be registered in the database if the file is lt 50M and 2 Files will be regist
3. Alignment the alignment of the table on the page The following options are available Left Center Right Cell spacing the space between individual cells as well as cells and table borders in pixels Cell padding the space between the cell border and its contents in pixels Caption the label of the table that is displayed on top otf it Summary the summary of the table contents that is available for assistive devices like screen readers 14 THE HEART OF OUR ELN Note 1 pixel px is approximatively equal to 0 30 millimeter mm With the ELN Chemistry plugin users can design chemical reaction which can be integrated in book pages reporting reused and changed if needed see chapter 5 1 3 A backup of your changes will be accessible until you save or cancel your new experiment or page You can also suppress this backup using the broom v a 17 23 45 22 17 23 51 17 23 57 17 24 02 4 2 The Book new sookroje ZETT Click on New Book Project button in the main menu Book Name Page Tags MILES EAS MES Tags You have to choose a name and add tags to help you with your search if you want Enter to validate each tag To validate use the button Submit 15 THE HEART OF OUR ELN pures Description Users having access collaborating Name Type E mail Anne Laure Sauvadet Owner sauvadet agilebio com Collaborator name prenom mail com Created by Anne Laure Sauvadet 2015 10
4. infection 2014 10 27 extraction 2014 10 27 m pierre 07 2014 07 01 20112014 book 2014 11 20 B EXP1 2014 11 20 Page 1 2014 11 20 m Book Nicolas 2014 12 12 lm scril23 2015 03 12 LL ALS 2015 10 06 G3 Irritation oculaire IO OCDE PH 15 02 B9 test WF 2015 10 06 2015 10 06 2015 10 06 Hide Show archived projects Collapse all Expand all Select Pages Users can hide or show archived books to refine the Tree View display Archived project are hidden by default The separation between the Tree View and the main panel is flexible To modify the tree view dimension click on the separation line between both panels and drag it on the left or on the right according to your needs 12 THE HEART OF OUR ELN 4 THE HEART OF OUR ELN 4 1 The Text Editor For description and content of main page you have to use the ELN text editor Description E source W amp m Dg 4 mia ana 4 FP O A3 R 5 Ah A E X syes Normal Don t hesitate to use the user s guide of the text editor CKEditor that you can open using m button About CKEditor A CKEditor CKEditor 4 3 1 revision 3ecd0b8 http ckeditor com Check CKEditor Users Guide for help For licensing information please visit our web site http ckeditor com aboutllicense Copyright CKSource Frederico Knabben All rights reserved If you want to insert pictures or use a text written in anothe
5. 10 OVERVIEW Use ASC DESC button to display information by ascending descending order By default Tree View elements are displayed by date of creation but you can sort them by alphabetical order Bs Tree Option Hide dosed pages Show Experiments and Pages created w from 2015 10 01 to 2015 10 01 Sort Books and Experiments 8 sort asc C Sort DESC Alphabetical sort The Tree View panel displays books experiments and pages Three tabs are available to manage the Tree View My Book default setting display all books created by the user My Collaborations display books for which the user has been identified as a collaborator A collaborator can view edit and modify experiments and pages All Books only displayed with Admin status display all books of the lab A Quick search engine by keywords is integrated allowing users to quickly find books experiments and pages Navigation between results is possible using Find Next and Find Previous 11 OVERVIEW ta By Searchby Keyword v BA My Books My Collaborations All Books gt Quick search Find Find Next Find Prev p sni sui y la Book T1 2014 04 15 LJ WNV 2014 05 19 BB infection 2014 06 17 1 2014 06 17 page 2014 10 16 LJ Project 1 2014 05 22 BB Exp rience 1 2014 05 22 Page 1 2014 05 22 Font test 2014 05 23 jm Book IS98 2014 06 19 la Book 012 2014 06 19 LJ 1598 2014 06 30
6. Windows_NT C Program Files x86 ImageMagick 6 COM EXE BAT CMD VBS VBE JS AMD64 Startup and Recovery System startup system failure and debugging information New Edit Delete cama Although copying DLL files from the PHP folder into the Windows system directory also works because the system directory is by default in the system s PATH this is ELECTRONIC SIGNATURES not recommended PHP folder is located in the main LabCollector folder for example C Program Files x86 AgileBio LabCollector php PHP will search for the openssl cnf using the following logic e The OPENSSL CONF environmental variable if set will be used as the path including filename of the configuration file The SSLEAY CONF environmental variable if set will be used as the path including filename of the configuration file The file openssl cnf will be assumed to be found in the default certificate area as configured at the time that the openssl DLL was compiled This is usually means that the default filename is c usr local ss openssl cnf Basically just create the folder C usrWocal ssl folder usr then local then ssl and copy openssl cnf provided in LabCollector php extras 7 2 Use electronic Signatures 7 2 1 Manage Certificates Go to ADMIN Manage Digital Certificates Certificates and Keys Create new user certificate and keys OpenSSL and Curl need to be active User Date
7. Small quality 40px 40px Medium quality 160px 160px Big quality 360px 360px You can also define rules to manage images usage Select an image file MLR New Box Image usage Panel dimensions can be modified using the Panel Editor You can define panel width and height quickly using your mouse You can also add a panel grid in the background facilitating elements alignments Click on the See Grid icon to display the _ Final volume after pool A 300 uL v THE HEART OF OUR ELN Each element added appears in a grey box allowing users to manage box dimension easily Note the box border and color aren t displayed when you print a preview paper version or pdf file report Diagram 7 En Sample Volume leaned lend Lana 800 uL Final volume after pool 300 uL The last tab Add New Molecule Item is optional appears only if you have the plug in and allows designing chemical structures and reactions You can choose to import structures from LabCollector Chemical Structures module or to design new structures directly from the Diagram Designer PR RT bie Add New Molecule Item 13 Edit panel width 600px Add New Molecule 400px 2000px See Grid To import structure from LabCollector database only Chemical Structures module you must link the page to structures of interest using Link LabCollector Data to this Experiment see chapter 4 3 When chemical structures are linked to t
8. WorkFlow Design Name PCR on environmental DNA Instructions Perform 3 different PCRs on extracted and purified DNA from environmental sample Predefined Task List PCR reagents aliguots Cleaning and UV in the hood 15 mL tubes and PCR plates UV Hood reservation thermocyler reservation Task Comment No of Steps Pages Page Templates in Workflow Page 1 Bacterial PCR Page 2 Archaeal PCR Page 3 Eukarya PCR Admin Validation Required Workflows are useful for routine experiments helping standardize writing of experiment reports to increase quality of lab activities A workflow is related to an experiment For each workflow you can predefine task list choose the number of page in your workflow and select a template for each page You can also decide if pages require admin validation or not 1 We recommend adding a couple of blank pages at the end of a workflow to avoid unexpected events even if length pages in the workflow are unlimited So users will be able to add rectifications if signed pages contain errors or need additional information TEMPLATES AND WORKFLOWS MANAGEMENT So when you start an experiment you just have to select the appropriate workflow Add New Experiment Experiment Name Biofilm sample LeafA1 58 Page Tags Tags Choose WorkFlow PCR on environmental DNA Your experiment details page will have a new section about workflow information Add New Page Bom sa
9. 08 11 13 07 Modified by Anne Laure Sauvadet 2015 10 08 11 13 07 n E Archive One the book creation finished you retrieve your information on the viewer You can edit the book s name tags and use the field description if needed Owner can now define several collaborators who will be able to view and modify the book Use the link at right Manage user s access to access to collaboration options With Basic Permissions Chapter 3 1 1 User Name Allow User Access t a Virology Microbiology Experiments Allow User User Name Group Access O Virology Microbiology K Administration LAM To unlock options for users tick the box Allow User Access then choose your different options for Book Experiment and Pages You can also define who can sign pages Your collaborators will see your book in the section My Collaborations For each book you have a menu on the top right You can Add New Experiment Chapter 4 3 Print Book Export in PDF or Zip format PDF attached files and access to the Book History 16 THE HEART OF OUR ELN The Book History displays all book page versions You can open and recover an old version by clicking on the book name It is useful to identify page modifications and therefore it promotes traceability of lab work The same versioning option is available at the experiment and page levels Books are the only items that can be archived Archive button You can choose to arc
10. for research projects technical platform service activities and company projects ELN add on can be fully integrated with LabCollector the LIMS we developed for life science research labs Pharma and biotech industries Indeed you can link information from LabCollector to an experiment and a page LabCollector is a copyrighted product from AgileBio GETTING STARTED 2 GETTING STARTED You can get ELN add on simply by downloading from www labcollector com LabCollector software has to be installed first as it contains the framework LabCollector support documents for installation are available on our website ELN add on can be installed on any operating system Windows MacOS X and Linux 1 Manual mode Unzip and paste ELN add on folder in the extra modules folder For Windows it would look like C Programs AgileBio LabCollector www lab extra_modules eln Open LabCollector the ELN add on module is now activated Click on the module to finish the installation 2 Automatic mode from LabCollector interface You can also use LabCollector Menu Admin gt Setup gt Upload Add Addons gt Upload Addon ZIP gt Add Addon Return to LabCollector the ELN add on module is now activated Click on the module to finish the installation The add on will remain in a 30 days free trial mode until you save the final license Admin gt Setup gt License To obtain a valid license you have to copy and send the activation key to AgileBio
11. functions see chapter 7 of this user guide 3 1 1 Permissions TOTO e Workflow gt lt Template m Log gt ES Page 75 Add Book Project Rules All Books Tab Access 53 File Uploads Jf Digital Certificates Jf Digital Certificates Options CJ License Through ADMIN Manage Advanced Permissions administrators can manage users permissions Basic selection corresponding to actual users permissions Advanced selection administrators can define PI for each group and specific user s permissions Basic selection opens two more tabs 1 Add Book Project Rules allowing administrator to select if user and staff can create new book OVERVIEW Add Book Project Rules Save 2 All Books Tab Access allowing administrator to configure access to All Books All Books Tab Access Full Access for Admin All Books O ON Read Write O OFF SPECIFIC Select Admin User Specific Access O O View Access for Staff All Books On Read OFF View Access for Users All Books On Read O OFF Advanced selection allows defining Pl for each group and permissions for all users Per user permissions are All All permissions C EW user can create and edit workflow C ET user can create and edit template ANB user can add new books VAB user can view all books OVERVIEW a Select Mode O Basic O Advanced Define PI nec vi Default Group v
12. p Options SpreadSheet Data Diagram Designer LabCollector Data Associated Files Available Custom fields for ELN Template Design Checkbox v Field Name Type Select list select Checkbox checkbox Access By default the template is shared with all ELN users Y Share with all ELN users Share with my group Share with other groups Share with other user s Select in the template options sections that you want to use in this template SpreadSheet Data Diagram Designer LabCollector Data or Associated Files Custom fields created in the previous step see chapter 5 1 1 can be selected here In the last section you can configure access to this template 5 1 3 Reaction template With the ELN Chemistry plugin in option users can design chemical reaction by importing structures from LabCollector Chemical Structures module TEMPLATES AND WORKFLOWS MANAGEMENT Chemical reactions can be integrated in book pages reporting reused and changed if needed You can design chemical reactions by clicking on the chemistry plugin available in the text editor b molecule Plot Pi ttt Molecule Add Insert in Page Save as Template Molecule Search Insertiarrow S Add Insert in Page Save as Template Once a reaction designed it can be inserted in book page and save as template TEMPLATES AND WORKFLOWS MANAGEMENT To manage reaction template you ha
13. v Date range from 2015 10 01 to 2015 10 01 User Date range Action Book Name Anne Laure Sauvadet 2015 10 09 Recover Content Book HYDROTHERMAL EXPERIMENTS Anne Laure Sauvadet 2015 10 09 Admin ARCHIVED book 2 TRASH Anne Laure Sauvadet 2015 10 09 Admin UNARCHIVED book 2 TRASH Anne Laure Sauvadet 2015 10 09 UPDATE Book Description HYDROTHERMAL EXPERIMENTS Anne Laure Sauvadet 2015 10 09 CREATE NEW Experiment Project 3 HYDROTHERMAL EXPERIMENTS SAMPLES User Moved experiment Generalities in book TRASH User Moved experiment Generalities in book DURESS 2015 10 09 2 TRASH 1 Generalities Anne Laure Sauvadet 2015 10 09 1 DURESS 1 Generalities The View Log Activity recorded the same information as Audit trail but only on the last 50 entries and without filtering og Entry View last 50 entries Date Book Name Experiment Name Page Name Owner 2015 10 12 3 HYDROTHERMAL EXPERIMENTS Biofilm sample Leaf 1 58 Archaeal PCR N 1585 CREATE NEW Page Anne Laure Sauvadet 2015 10 12 Admin EDITED Template Archaeal PCR Anne Laure Sauvadet 2015 10 12 Admin CREATED C Field Grid Anne Laure Sauvadet 2015 10 12 HYDROTHERMAL EXPERIMENTS Biofilm sample LeatA1 58 Bacterial PCR N 1584 UPDATE Page Description Anne Laure Sauvadet 2015 10 12 3 HYDROTHERMAL EXPERIMENTS Biofilm sample Leaf 1 58 Bacterial PCR N 1584 CREATE NEW Page Anne Laure Sauvadet 2015 10 12 3 HYDROTHERMAL EXPERIMENTS Biofilm sample Leaf 1 58 CREATE NEW Experiment Project Ann
14. 00 96 0 00h OPEN 100 00 0 00h 2015 10 12 0 00h CLOSED 2015 10 12 0 00h 100 00 0 00h CLOSED wo sooo 8h son ise Sh Total time Total time ELECTRONIC SIGNATURES 7 ELECTRONIC SIGNATURES Validation with electronic signature certifies the ELN contents and all links between the ELN and LabCollector Database Before using digital certificates LabCollector need to be setup 7 1 Manage Electronic Signatures First activate OpenSSL and Curl on your PHP preferences Windows open LabCollector Manager in Settings gt Configure Servers gt PHP edit PHP INI and uncomment delete the following extensions extension php_openssl dll and extension php_curl dll Mac contact us for more information Linux install PHP OpenSSL and PHP Curl rpms For Win32 64 users in order for these extensions to work two DLL files libeay32 dll and ssleay32 dll must be available to the Windows system PATH System32 or SysWOW64 For information on how to do this see How do add my PHP directory to the PATH on Windows Computer Name Hardware Advanced System Protection Remote User variables for AgileBio You must be logged on as an Administrator to make most of these changes Variable Value USERPROFILE AppData Local Temp USERPROFILE AppData Local Temp Performance Visual effects processor scheduling memory usage and virtual memory User Profiles Desktop settings related to your signin Value
15. La bCollector User Guide Electronic Lab Notebook ELN Version October 2015 2015 by AgileBio www agilebio com amp www labcollector com Summary INTRODUCTION GETTING STARTED OVERVIEW 3 1 Admin Menu 3 1 1 Permissions 3 1 2 File upload options 3 2 Option Menu 3 3 Tree View THE HEART OF OUR ELN 4 1 The Text Editor 4 2 The Book 4 3 The Experiment 4 4 The Page 4 4 1 Spreadsheet Data Need JAVA Plugin 4 4 2 Diagram Designer TEMPLATES AND WORKFLOWS MANAGEMENT 5 1 Templates 5 1 1 Create custom fields 5 1 2 Page template 5 1 3 Reaction template 5 1 4 Spreadsheet template 5 2 Workflows AUDIT LOG ACTIVITY AND TASK TIME ELECTRONIC SIGNATURES 7 1 Manage Electronic Signatures 7 2 Use electronic Signatures 7 2 1 Manage Certificates 7 2 2 Page validation and signing 8 UPGRADING AND UPDATING INTRODUCTION 1 INTRODUCTION Tank you for choosing one of AgileBio s solutions for the management of your lab The ELN add on is a web based solution allowing efficient management of all your experiments in the lab Unlimited number of books experiments and pages can be created Powerful tools are included to produce added value notebook Text Table Interface Log Activity Mass Doc Picture Molecules Import tools Electronic Signatures Chemical reaction Diagram Designer Task time reports Versioning Template Workflow management Pdf Print Zip export The ELN provided by AgileBio is suitable
16. Private Key Public Key CSR Emilie 2013 09 27 15 52 51 Tiago 2014 12 11 19 06 00 Nicolas 2013 11 19 17 36 02 EXPIRED ALS 2015 10 13 16 51 25 365 days From this page the administrator can create and manage all digital certificates Click on Create new user certificate and keys at the top left dla All fields are required to create the certificate A certificate is unique and related to only one user Once submitted user profile is displayed on the screen Three keys are created Private Key Public Key CSR Certification Signing Request ELECTRONIC SIGNATURES ems A signature image can easily be attached to the certificate Just download it using icon A certificate is valid during one year It can be renewed by a simple click on RENIEW button Authentication can be configured at this stage via Admin gt Manage gt Digital Certificates Options e Login Authentication authentication with your LabCollector login e Certificate authentication by password only authentication with the password generated when you create your digital certificates Certificate authentication by private key plus certificate password as previous Certificates and keys options for signatures Choose the Authentification Mode No Authentication C Login Authentication Certificate Authentication Certificate Authentification Mode O Private Key Password 7 2 2 Page validation and signing Workflows are edited w
17. ame Page Name Action Anne Laure Sauvadet 2015 10 09 13 13 07 Week 31 2012 test deletion v Sign Page Anne Laure Sauvadet 2015 10 12 17 49 44 Biofilm sample LeafA1 58 Archaeal PCR N 1585 Anne Laure Sauvadet 2015 10 14 11 12 47 test sign Anne Laure Sauvadet 2015 10 14 11 38 53 test sign Anne Laure Sauvadet 2015 10 14 11 57 54 test sign Sign all listed pages at once UPGRADING AND UPDATING 8 UPGRADING AND UPDATING To update or upgrade the ELN Add on module just download it from our website www labcollector com Then unzip the folder and paste files in the following folder Programs AgileBio LabCollector www lab extra_modules eln The name of this folder is the laboratory nickname chosen during LabCollector installation AgileBio USA 1133 Broadway Suite 706 New York NY 10010 http www agilebio com USA Tel 347 368 1315 Fax 800 453 9128 AgileBio Headguarters 75 rue de Lourmel 75015 Paris FRANCE Tel 01 41 79 15 85 Fax 01 72 70 40 22
18. arator Update Values For select list and checkbox types edit the values with icon The grid field type allows creating a two column table that you can fill with the values of your choice X Cancel Add row Add 10 rows i Remove selected Clear all i Import CSV Export CSV 5 1 2 Page template Add Template Search By Name MM by User from yo MN Ee Default template version 3 Default Bacterial PCR version 4 Archaeal PCR version 3 eem PCR version 1 On this page you can manage all your templates Create a new template with Add Template button or view edit an existing template selected in the list with the View Edit buttons On the same page you have the versioning data for each template The template is identified by a name and a description if needed You can use the text editor to prefill your page TEMPLATES AND WORKFLOWS MANAGEMENT 5 Edit Template Template Name Bacterial PCR Template Description PCR with General primers Prefilled Page Content El Source W Sls BI mam d pie E E e a e d m Styles Normal Protocol thermocycler according to INSERT REFERENCE Temperature Time Cycle Positive control gt Runella slithyformis 95 C 2 1 94 C 30 52 C 30 72C 90 1 cycle PCR on extract and concentrated DNA from ADD DATE ADD EXPERIMENT PAGE with bacterial primers 27F U1492R on ADD EQUIPMENT Conclusion body
19. e Laure Sauvadet AUDIT LOG ACTIVITY AND TASK TIME The Task Time function allows you to visualize time required to perform project tasks This report can be edited for a user a period and completed tasks Export file is available with the icon Ss This feature is very useful for collecting task s time and user s time per project AND User Select Book Name HYDROTHERMAL EXPERIMENTS HYDROTHERMAL EXPERIMENTS HYDROTHERMAL EXPERIMENTS HYDROTHERMAL EXPERIMENTS HYDROTHERMAL EXPERIMENTS HYDROTHERMAL EXPERIMENTS HYDROTHERMAL EXPERIMENTS Experiment Name SAMPLES SAMPLES Biofilm sample LeafA1 58 Biofilm sample LeafA1 58 Biofilm sample LeafA1 58 Biofilm sample LeafA1 58 Biofilm sample LeafA1 58 v AND Date range from 2015 10 01 to 2015 10 01 User Anne Laure Sauvadet Anne Laure Sauvadet Anne Laure Sauvadet Anne Laure Sauvadet Anne Laure Sauvadet Anne Laure Sauvadet Anne Laure Sauvadet Task name Samples sorting Experiment workflow PCR reagents aliquots Cleaning and UV in the hood 1 5 mL tubes and PCR plates UV Hood reservation thermocyler reservation Date start 2015 10 09 2015 10 09 2015 10 12 2015 10 13 2015 10 13 2015 10 12 2015 10 12 O Only show complete experiments FESE xz Date stop Time Completion Executed time 2 00h 20 00 O40h OPEN 2 00h 50 00 100h OPEN soon soon 0h 3 00h 75 00 225h OPEN Total time 1 00h 0 00 0 00h OPEN 100h 0
20. e home page refresh your internet browser page to be able to see your new experiment page Folder icon in the tree For each experiment you have a menu on the top right You can Add New Page Chapter 4 3 Print Experiment Export in PDF or Zip format and access to the Experiment History Experiment can be moved from a book to another using the related button Move Experiment To right bottom of the experiment details 1 Since you cannot delete experiment we recommend you to create a book TRASH and move the experiment that you don t want to keep inside By default the experiment page has two more sections Task list LabCollector Data Box Microplate is only available in Pages Task list Add task list item gt by Anne Laure Sauvadet 2010 02 11 Samples sorting Task Start Date 2015 10 01 Duration h Percent Complete I The task list can be edited to follow up experiment advancement 18 THE HEART OF OUR ELN Each task is defined by a name a date duration and a ratio A graphical view of tasks can be displayed using Gantt chart option i Tasks definition will allow you to edit task time and allocated resources reports for a project For more information see chapter 6 SAMPLES lt Save Change Gant Chart Users can also link LabCollector data to the experiment allowing a complete traceability of laboratory activities 4 4 The Page Click on Add New Page bu
21. ered in the defined folder if the file gt 50M 3 2 Option Menu From the Options menu you can select to display ELN interface in English French German or Portuguese Tree View management options are available in this tab see chapter 3 3 OVERVIEW New Book Project Add Log Entry Aa Options Language Ps Tree Options Tt a Show Hide Tree IP Merge Selected Pages print Cul Merge Selected Pages pdf Through this menu you can also access to tools to merge compile two or more pages in print pdf views report arrangement To select interesting pages click on the Select Pages bouton and check pages 20112014 book 2014 11 20 S EXP1 2014 11 20 o Page 1 2014 11 20 im Book Nicolas 2014 12 12 ja scril23 2015 03 12 LL ALS 2015 10 06 amp 3 Irritation oculaire IO OCDE PH 15 02 B9 test WF 2015 10 06 is 2015 10 06 M 2015 10 06 Hides Show archived projects Colapse ail Expand al Sect Pe Then choose your printing method PDF or print through the Options menu click on merge selected pages print or merge selected pages PDF 3 3 Tree View You can hide the tree view using ta or display the Tree View options using Pa next to the search menu or from the Menu bar Options gt Tree Options Several options are available to manage information displayed in the Tree View Hide closed pages Display only created or modified pages Select a time period
22. f their work New Book Project Add Log Entry Options ADMIN Workflow a 5 Template ho Log k ES Page 5 1 Templates 5 1 1 Create custom fields To customize ELN pages and ELN pages templates users can create custom fields Go to Admin gt Template gt Manage custom fields Pool of fields 6 Refresh List Field Name Type Actions Templates using it Mandatory Help text 1 Selectlist select Sar NO 2 Checkbox checkbox Sar NO Add New Custom field into Pool of fields Field Name Type o Free text field Checkbox Select list Date Field Link Field Grid Field Mandatory O Yes No Help text Options for Text Field type Length 50 vi Add Custom Field Note if you want defined parameters fields to be added to the template you need to select an available custom field from the list above or generate a custom field first and select it To add a field choose a name and define the field type text checkbox select list date link or a grid Maximum length of a text field is flexible depending on reguired information It is possible to define a custom field as mandatory With this function you will be sure that required information will be completed To help your colleague to understand the data reguirement use the help text section TEMPLATES AND WORKFLOWS MANAGEMENT Edit predefined values for type is select values list NOTE Do not use as it is used as a sep
23. he ELN page the tab displays the list of available structures Select one structure to add it directly in the panel 25 THE HEART OF OUR ELN LabCollector Data Name Vitamin C F zas SpreadSheet Data Diagram Designer TL EEE Edit panel width 600px ml 7 Add New Molecule height Users can also design their own chemical structures directly through the diagram designer using Add New Molecule function using the open source editor JChemPaint File Edit View Atom Bond Tools R groups Templates Exe S S l amma Ge mole 2015 10 13 12 36 28 Submit Cancel p Jl E LG ROW OOO b N o md c amp o NJ e s LEJ cu Br 1 S11 A new window containing a molecule editor appears You can now design any molecule needed for your experiment This tool includes a molecule database with the most used ones Templates A periodic table is also integrated When the molecule is designed define a name and click on Submit button to display it in the THE HEART OF OUR ELN panel Molecules in the panel can be modified using Edit function in the molecule box grey 27 TEMPLATES AND WORKFLOWS MANAGEMENT 5 TEMPLATES AND WORKFLOWS MANAGEMENT To make AgileBio ELN friendly to use template and workflow functions are integrated These options allow users to save time and use standard procedures to increase productivity and quality o
24. hive them when they are not used or finished This feature allows you to hide books in the tree view to ensure quicker navigation If you want to find an archived book simply check the Show archived projects box in the tree view You can unarchive a book by selecting it and use the Unarchive button 4 3 The Experiment Click on Add New Experiment button in the main menu You have to choose a name and add tags to help you with your search if you want Enter to validate each tag You can also decide to use a workflow To validate use the button Submit a Add New Experiment Experiment Name SAMPLES Page Tags CHEMECO x J HYDROTHERMAL x ME Tags Choose WorkFlow Default No workflow A workflow is useful when the lab executes routine experiments A workflow is defined by a page number Each page of the workflow can be a standard page or a predefined template Workflow and template creation are described later in the document see chapter 5 17 THE HEART OF OUR ELN SAMPLES Experiment type DEFAULT Description Task list Add task list item Box Microplate LabCollector Data Link LabCollector Data to this Experiment Created by Anne Laure Sauvadet 2015 10 09 10 29 55 Modified by Anne Laure Sauvadet 2015 10 09 10 29 55 am Once the Experiment creation finished you retrieve your information on the viewer You can edit the experiment s name tags and use the field description if needed dla Once on th
25. ited and modified from the Admin Menu see chapter 5 1 4 To edit a spreadsheet click on the can icon to insert tables From this panel you SpreadSheet Data No SpreadSheet Data are link to this page You can e add a new one without template e add a new one whith the template Gradient PCR ok e adda new template When the spreadsheet is opened you can edit modify tables and graphics to store your results Users must save tables into the database otherwise information will be lost 22 THE HEART OF OUR ELN as SpreadSheet Data Full screen Cancel changes Save into database J Delete File Edit View Insert Format Tools Help BSH 8 s BAS oc m v4 NOM SensSerif viwy B Zz u A 2228 lH2 wo A1 Temperature Gradient A Tio HA AM ENS SON PEER ESET UA VA WAX EAA EAC HAD T moin positif 1 10 T moin positif 1 1 Torney o je a 65 1 65 5 Nitubes Batch O SSS eau Low sms ms ne ne ne ns ns npe ne ns ns na ns me ns ns ns ns me 115 MgCI2 pmo 2 2 2 2 2 2 2 212 2 2 2 2 2 2 2 2 2 2 2 2 2 Buffer bit dNTP new 07 07 07 07 o7 07 07 o7 07 07 o7 o7 07 07 07 07 07 07 07 07 07 eukF 454 Ci 10M A ED GE DE tt eukR 454 Ci 104M GoTag Vol Prod aaa aa aparecia al Vol ds Tube 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 2 20 20 20 20 o N E mM olololo lu in N wo
26. ith two options page validation signing or not as it was describe before Chapter 5 2 Go to Admin gt Page gt Page Validation amp Signing A list of all pages that need to be approved closed is displayed The administrator can approve pages only if it s required by the workflow The approval is indicated by a name and a date in the bottom of the page When a page is validated no changes are possible ELECTRONIC SIGNATURES how only pages from user Select User Book Name Admin Status PlerreLab 2009 12 21 10 19 1 Workflow test workflow PENDING PlerreLab 2009 12 21 10 20 25 Workflow test workflow PENDING PierreLab 2010 03 05 16 37 14 Workflow test workflow Page 3 PENDING PlerreLab 2 se thtyhtyh fvdfvdfvdf VVVVVVVVVVV PENDING PlerreLab 2 T thtyhtyh fvdfvdfvdf bbbbbbbbbbbbb PENDING Copyright AgieBio 2007 All Rights Reserved ELM v 1 61 If no validation is required users can close their pages directly without admin validation Once a page is closed user can sign it to certify the page content Then the page is signed by the administrator to complete the certification process of the document Administrators that can sign are the same users define as Pl in section Advanced Permissions They can find a list of all pages to sign in Admin gt Page gt Page Signing F Closed Pages awaiting Admin Signing Show only pages from user v ano Book MEZA ES vou cannot sign your own pages User Date Book Name Experiment N
27. mple Lea Experiment type In Workflow Worflow Information Uses Workflow Workflow Instructions PCR on environmental Perform 3 different PCRs on extracted and purified DNA from environmental DNA sample Page Status gt by Anne Laure Sauvadet 2015 10 12 PCR reagents aliquots gt by Anne Laure Sauvadet 2015 10 12 Cleaning and UV in the hood gt by Anne Laure Sauvadet 2015 10 12 1 5 mL tubes and PCR plates UV gt by Anne Laure Sauvadet 2015 10 12 Hood reservation gt byAnne Laure Sauvadet 2015 10 12 thermocyler reservation Box Microplate LabCollector Data Created by Anne Laure Sauvadet 2015 10 12 14 28 15 Modified by Anne Laure Sauvadet 2015 10 12 14 28 1 And the creation of the pages in your experiment will be automatic following the workflow Add New Page In WF Choose Page Template Type Bacterial PCR Page Name Bacterial PCR N 1584 Page Icon ODOBOHOMOUO4OBOBOAMKOHOVJ Page Tags Tags AUDIT LOG ACTIVITY AND TASK TIME 6 AUDIT LOG ACTIVITY AND TASK TIME The audit function allows team leader to follow up users activities on the ELN COTOS e z Workflow LEE tr Template View Log Activity CI Page p E Task time 26 Manage The Audit Trail displays all modifications done by the selected user in a specific date range Numerous actions are identified like page creation edition signing link removal etc Audit Trail Log User Select
28. r text editor our advice is to use the different paste buttons the paste content applet add an image and the link to LC Photobank BRE amp l O 4 B 8 If you want to modify an image before insert it you have to use the paste content applet and chose the option Send to MS paint So you can add legends text box arrows 13 THE HEART OF OUR ELN M saros a l BFO mo a POD ON CO na nF gt JI Send to MSPaint Reload clipboard If users need to import tables they can use the mouse right click but we don t recommend it It s better to create a new one and fill results manually Press the button on the toolbar The Table Properties dialog window that will open lets you set configuration options that define table size its display properties or other advanced properties Below is an overview of all Table Properties tab elements e Rows the number of rows in the table obligatory e Columns the number of columns in the table obligatory e Width the width of the table in pixels or a percent value Giving the width as a percent value lets you set the proportion of the editing area that the table will occupy Height the height of the table in pixels Headers the drop down list that formats certain table cells as headers which applies special formatting to them You can apply header formatting to First Row First Column or Both Border size the thickness of the table border in pixels
29. tton in the main menu If no workflow is applied to the experiment you can choose a page template in the list if needed If a template is applied the page is formatted using the predefined template allowing users to save time just follow template instructions see chapter 5 Then you have to choose a name and add tags to help you with your search if you want Enter to validate each tag The page can also be associated to an icon for quick identification in the Tree View Several icons are available Those icons have no special meaning Just define with your team relevant signification for each icon It can be standard page process sequence analysis calculations etc 19 THE HEART OF OUR ELN Choose Page Template Type Page Name Page Icon JOBOHOMORO4O8OHO Page Tags Tags Once the Page creation finished you retrieve your information on the viewer You can edit the page s name tags and use the field content to describe your experiment For each page you have a menu on the top right You can Delete the page Print Page Export in PDF or Zip format and access to the Page History da Page deletion is possible only if the section Content has never been saved version 1 You can view version number on the top left This number change after each content page edition dla Please note that user can t edit a page if already open by another user lock page on editing All buttons turn grey By defa
30. ult without template the ELN page has several sections Box Microplate LabCollector Data SpreadSheet Data see section 4 4 1 Diagram Designer see section 4 4 2 Associated Files THE HEART OF OUR ELN G version 1 lt lt Gen CR a Akh Content Box Microplate Admin Validation Reguired Page Status and Signatures Created by Anne Laure Sauvadet 2015 10 09 12 39 04 Modified by Anne Laure Sauvadet 2015 10 09 12 39 04 G Close Sign Page To access to a box microplate directly in your ELN you can link a box using the corresponding section Select your storage place then your box Once save you can chose between box view and list view Y Save Cancel Select Storage Place Select storage location Select Box Name Primers ALS Box Microplate PRTA DRR TT ee ee Le LLL do dl de Jr s GEO Y In the section Associated Files files can be attached to the page and its status version can be defined definitive SP intermediate 6a or discarded 9 version 21 THE HEART OF OUR ELN All page content modifications are allowed until the page is closed signed This option is very useful to be compliant with a QA management system Refer to chapter 6 for more details 4 4 1 Spreadsheet Data Need JAVA Plugin Use a blank spreadsheet editor to create your own tables Create a spreadsheet template to be used in routine Load a spreadsheet template Spreadsheet Templates can be ed
31. ve to go in Admin gt Template gt View Edit Reaction Template Here you can edit your reaction with 3 and delete a reaction with G View Edit Reaction Template M Search Description Created By Tiago 2015 10 13 14 03 33 Last Update By Tiago 2015 10 13 14 03 33 TL Description Created By Tiago 2015 10 13 13 08 52 Last Update By Tiago 2015 10 13 13 08 52 Description Created By Tiago 2014 11 20 13 47 39 Last Update By Tiago 2014 11 20 13 47 39 AAAA o M M 5 1 4 Spreadsheet template View Edit Delete Add SpreadSheet Template Choose Template to View Edit Gradient PCR v RANTE EA E ISE From Admin gt Template gt Manage SpreadSheet Template you can manage spreadsheet templates You can add new templates from this panel or you can view edit templates saved in the ELN application TEMPLATES AND WORKFLOWS MANAGEMENT Template name File Edit View Insert Format Tools Help Pao 8 BRAY gt amp 100 v SansSerif v v rat eo oo u ao on i wir gt u m 4 Sheet Ready E 5 2 Workflows A workflow is a sequence of connected steps that can be used in a work organization or a process From the Admin menu the administrator can add edit a workflow combining several pages blank pages and or templates that will be applied in an experiment d Before editing workflow you need to define page templates if needed chapter 5 1 TEMPLATES AND WORKFLOWS MANAGEMENT
32. wo e N DOIN OD Om BUN o P olololo zn mM o o o o m 3 o To Co C0 4 Mo U r2 71 ao ooo N o mM olololo MES ED 20 a N o 4 Sheet Ready A Formulas are allowed but they must be written in English format French isn t recognized A Formulas are working with commas instead of dot in decimal numbers Now you can download your spreadsheet as an excel file by clicking on the Excel icon at right Spreadsheet data are also integrated in the printable PDF and zip versions 4 4 2 Diagram Designer El LabCollector ELN integrates a Diagram Designer Click on this icon E and Create to start a diagram To print a paper version or see a diagram review use the tab Other Multiple elements can be added like arrows tubes etc Diagram Designer Add Item Add Personnal Item New Text Box O E O 2000px wb New Arrow DE Y New Down Arrow o cd New Left Arrow New Left AccoladeNew Left Accolade t New Up Arrow W New Left Down Arrow New Empty Tube R New Left Up Arrow New Tube NW New Right Down Arrow New Empty Erlenmeyer New Right Up Arrow i 2 New Double Arrow 34 New Special Arrow 1 gt New Special Arrow 2 gt New Special Arrow 3 23 THE HEART OF OUR ELN Images can also be added using Add Personal Item tab Select the image of your choice give it a name and choose the size Items can be imported in three resolutions
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