Download the Quick Reference Book: LabCollector Manual

Quick Questions:

1. How to create or edit records?
2. How do I customize record options?
3. How do I define and manage users access?
4. How do I link records and for what purpose?
5. How do I manage vendors and sellers?
6. How do I print barcode labels?
7. What is the formula that LabCollector uses for primers Tm?
8. How do I delete data?
9. Can I see/list all records?
10. Can I import data from external sources (Excel, FileMaker)?
11. New categories/options are not listed in the drop down menus?
12. How to install and use Chime on Firefox, Mozilla or Netscape under Windows?
13. How do I install Add-on modules?
14. How to use digital signatures on ELN?
15. How to use AD or LDAP login?
16. How to create custom fields?
17. How to create custom modules?

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Answers:

1. How to create or edit records?
   In each module, you can search and browse through data. On each record simply click on the edit icon (represented as a pencil on a blank page). To add new records, click on the link "New Record" on the top right of the page.
   
2. How do I customize record options?
   All options and parameters are defined on preferences section on Admin menu. There you can define all options that fit your laboratory activity. In admin menu you'll define also users privileges and software setup..
   
3. How do I define and manage users access?
   The first time you open LabCollector, there is only a super-administrator access. You'll have to enter staff names and contacts (on admin menu>>Manage Staff).Then associate those staff contacts to user logins and privileges (Admin>>Manager Users). Only the super-administrator can create new users or change them.
   NOTE: You need to associate the super-administrator login to a real person!
   
          Administrators = Can add and manage data on the name of any staff. It can manage waiting data list
          Staff = Can add and manage data on its own name only. Cannot manage others' data. Data is automatically approved.
          Users = Can add and manage data on its own name only. Cannot manage others' data. Data is not pre-approved and is added to the waiting list (for administrator's review).
          Visitors = Can only browse, search and see data.
   
4. How do I link records and for what purpose?
   The linking feature is very useful to associate separate records between them. For example, you may want to know that a particular antibody used on the lab is purchased to a commercial provider, at a particular price and that it exists on different lots and quantities on the lab. This is done by linking the antibody record to a reagent record containing all extra data. You may also want to tell that a home made reagent (entered as one reagent record) is made of several other reagents listed on the database. In this case you link the first reagent record to all other reagents records. This way, you can quickly browse through all records.
   To link records, use the memorization button. Search all separate records that you want to connect to a main record and on each, click on the associated memorization button (represented as clipped papers). Once this made, open the main record and click on the "link to other data" button represented as a green + sign on a paper. You can choose from linking to the same record category or to external data. This helps understanding links once done. You will be redirected to a confirmation page where you can control the memorized links and approve them or not. In this page you can also delete existent links for this record.
   
5. How do I manage vendors and sellers?
   Since LabCollector 3.6 and up, vendors can be managed from the new address book module or the old-style built-in table. The "super administrator" can manage this choice that will apply to the reagents and equipment modules. If data was already entered in those modules, you will need to edit them to link to the new address book entries.
   
6. How do I print barcode labels?
   From Internet Explorer you can print the barcode image directly to any printer by right-clicking on the image and use "Print image" on the contextual menu. From other browsers, click on the barcode image to open a new window containing the barcode image only and then print the page. You can use any label printer.
   
   You can also get pre-printed barcode labels from Agilebio and use them directly with LabCollector easily without time consuming printings. Our labels are resistant to hard conditions like extremely low temperatures (cryolabels)
   
7. What is the formula that LabCollector uses for Tm?
   Two standard approximation calculations are used.
   For sequences less than 14 nucleotides the formula is:

   Tm= (wA+xT) * 2 + (yG+zC) * 4

   where w,x,y,z are the number of the bases A,T,G,C in the sequence, respectively.

   For sequences longer than 13 nucleotides, the equation used is

   Tm= 64.9 +41*(yG+zC-16.4)/(wA+xT+yG+zC)

8. How do I delete data?
   From v3.7 data can be deleted from LabCollector interface. This action can be performed by administrators and data owners. Deletion is made using the Delete Icon on the icon tray of each record. It is available only if no storage and cross-links are defined. You have to remove storage and links first. You can also delete storage boxes if they are empty. Categories and options can be removed if they are not in use. From v3.8 you can delete record ranges automatically or multiple records selected in memory.
   
9. Can I see/list all records in a module?
   Yes. Just do a blank search with no keywords.
   
10. Can I import files from other programs (Excel, Filemaker...)?
    Yes. In Admin menu >> Data >> Import you have specific interfaces for each module. You can import data from external sources that are formatted as described for each module. Importation files must be ASCII or Text files. So, you have to export to text files first from the original software (ex: CSV, tabulated text...). LabCollector accepts any kind of field separator (but those separation characters cannot be present inside fields).
    Since v3.9 you can also import SD chemical structure files and FASTA sequence's lists..
    
11. New categories/options are not listed in the drop down menus?
    This may be due to the cache. Force browser cache refresh (Ctrl+F5 in IE).
    
12. How to install and use MDL Chime on Firefox, Mozilla
    or Netscape under Windows?
    MDL Chime is the browser plugin that displays macromolecular structure, and is required for viewing the resources at MolviZ.Org and for Protein Explorer.

    The procedure for installing Chime into Netscape 7.2 (or Mozilla or Firefox), is a simple "manual" installation that can be performed only after using the automatic Chime installer on Internet Explorer. We're aware that this sounds kind of strange, but it works—read on.

    1. Printing this page now will be useful because you'll have to close the browser during the installation.
    If necessary, download and install Netscape 7.2 (or Mozilla or Firefox), available from the Netscape Product Archive (or www.mozilla.org or www.getfirefox.com).
    2. Download the MDL Chime installer, and first install Chime in Internet Explorer. (Yes, really.) Here are step by step instructions.
    3. After the installation into Internet Explorer, copy the file npchime.dll
    * from c:\Program Files\Internet Explorer\Plugins
    * to c:\Program Files\Netscape\Netscape\plugins
    (or c:\Program Files\mozilla.org\Mozilla\plugins
    or c:\Program Files\Mozilla Firefox\plugins).

    (The other three "chime" files in the plugins directory are unnecessary: chime.html is the Chime release notes; chime26.isu and ChimeShim.dll are obsolete.)
    4. Close all browser windows. This is necessary since browsers load plugins only when starting.
    5. Start Netscape 7.2 (or Mozilla or Firefox). Open the Help menu, and display About Plugins. If MDL Chime is not listed, the file npchime.dll was not copied into the correct directory -- return to step 3.
    6. Test your Chime installation on the structures module to make sure it works. Follow the link there for troubleshooting if necessary.

13. How do I install Add-on modules?
    First you need to have LabCollector v3.912 or later running. Then just download Add-on packages and unpack them into /extra_modules folder of your LabCollector. Next, enter into LabCollector and you'll notice that the new modules will be active. On the first access to the Add-ons you will be prompted to finish installation automatically.
    
14. How to use digital signatures on ELN?
    In order to use this feature, you need to activate OpenSSL and Curl on your PHP preferences. In Linux, install PHP-OpenSSL and PHP-Curl rpms. On windows and with our automatic installer, edit PHP.INI and uncomment extensions for OpenSSL (extension=php_openssl.dll) and Curl (extension=php_curl.dll).
    .
15. How to use AD or LDAP login?
    If you have a Windows AD or LDAP users management system, you can use it with LabCollector. In Admin>>Setup section you can define the AD or LDAP settings. Then you need to create users in LabCollector with exactly the same user name as in your AD or LDAP directory. No password will be defined in LabCollector as it will be provided by AD/LDAP. For security reasons, super Administrator is not managed by AD/LDAP.
    
16. How to create custom fields?
    In LabCollector you can extensivelly customize every module by adding a large variety of fields. This is done on Admin>>Data>>Custom Fields. These fields can be of several types like text, select menus, checkboxes, URL and even files. These additional fields can even be classified and grouped in order to show up only in certain types of records.
    
17. How to create custom modules?
    If you need to save specific types of records not well suited on the built-in modules, you can create full modules by your own. First you need to order this option to us to be able to enter the module's design tool. Next, enter it in Admin>>Data>>Custom modules. A module is defined by a name, a 2 letter code and an icon. A few options can also be linked, like the usage of the storage system if you need to store tubes.