GenoLogics LabLink-getting started
This system may also be referred to as Proteus.
To start, you will need an account which can be requested at:
http://128.143.19.247:8080/lablink/Login.do and click the Request a User ID tab on the left side of the screen.
If you have forgotten your account information, contact the lab (434-924-0070) to determine your login. Names are case sensitive.
After logging in, there are directions for the installation here on the left side of the page or go or directly to: http://proteus.achs.virginia.edu:8080/glsstatic/lablink/Help/Manuals/Proteus_Directions.pdf
New users need to complete the sign up page as described in the directions listed above.
Sample Submission
To submit a sample, log on to LabLink and click on the Submit Samples tab on the left side of the screen (green outline in screen shot above).
For instructions on completing forms, click on the link Get instructions, forms and templates for submitting samples on the left side (red outline in screenshot above) or go directly to:
http://128.143.19.247:8080/glsstatic/lablink/Help/Manuals/Proteus_Directions.pdf
For a single sample, fill out the form which appears. For multiple samples, download the appropriate spreadsheet at the above link.
If there are error messages, sample information will not transfer into the Proteus system.
If you have problems or questions, please contact the Keck MS Lab staff.
Viewing Data
To see your data, log in to GenoLogics LabLink. On the page which appears, in the drop down list next to View samples with status, select Invoiced and click the Apply box. Then click the Files tab.
Several file types are familiar. Notes on some file types are below.
Docx, xlsx
docx, xlsx files are created in Microsoft Office 2007. A converter program from Microsoft will make most, but not all, features readable with earlier versions of Office at: http://www.microsoft.com/downloads/: look for Microsoft Office Compatibility Pack. After installing, run Microsoft or Office update to update the converter program.
At the University of Virginia, Office 2007 can be installed under a Campus Agreement with Microsoft through ITC.
sfd and Scaffold
Files with extension .sfd were created with Scaffold.
You can download a viewer version of Scaffold software at:
http://www.proteomesoftware.com/
with versions for Windows, Apple OS, Linux; the Windows version is a 60MB download.
On the download page is a note on installing the viewer only version.
- Clicking on a file with extension .sfd will launch Scaffold (during Windows installations, Scaffold is set to open .sfd files).
- outside the University of Virginia, dowloading the .sfd file from Lablink, opening Scaffold and then opening the file may be necessary rather than automatically opening Scaffold within Lablink.
- Scaffold versions change relatively frequently so look for a new version if files do not open.
- If Scaffold is running in a Windows limited user account, there may be an error message about lack of access to some files-it seems that this message can be ignored for viewing; giving limited users write permission on the \Program Files\Scaffold folder eliminates the messages.
- On a several year old computer, loading a 97MB data file took 2 minutes, a 320 MB data file (14 samples) took 7'; then for Scaffold to display data took about 8' for the 97MB file, 37' for the 320 MB files.
Copying data from pdf files to other programs
Text-Short sections:
In Acrobat Reader, point and click to select text. If that does not seem to work, go to Tools-Select & Zoom-Select Tool (Acrobat Reader version 8). In earlier versions, it may be a Text Tool.
Insert into document
The text will probably have the same formatting as the original text.
To have default formatting for text in Microsoft Word, use Edit-Paste Special-unformatted text (if this is a common operation, you can find or write to macro which can be assigned to a shortcut key).
Big blocks of text
In Adobe Acrobat reader 8, use File-save as text. Previous versions may be different.
The file will have extension .txt, no formatting. Each line with have a paragraph marker at the end.
To do a mass remove of paragraph markers, in Microsoft Word, use Find and replace command (Ctrl-h). For find what, enter ^p ( caret p as shown, not Ctrl-P)
For replace with, try nothing. If words are run together, undo change, and for replace with, press space bar once to replace paragraph markers with a space.
For these operations, it can be helpful to show formatting marks (In Word, Tools-Options, View tab, and select all formatting marks.)
Pictures
The snapshot tool will copy selected parts of a pdf file, including a mix of text and pictures. In Acrobat Reader 8, go to Tools-Select &Zoom-Snapshot Tool. What is pasted is an image, so the text cannot be easily edited, or perhaps not edited at all.
Adobe describe methods for selecting an image only with the select tool and copying it. With the files produced from the MALDI software, currently these methods are unsatisfactory, giving rotated, distorted images which may only show in some programs.
PDF Creation programs such as Adobe Acrobat (not reader) can save pdf files in different formats, such as tiff and other image file formats. For information about purchasing a license for Adobe Acrobat through Research Computing Services, see:
https://www.web.virginia.edu/rescomp/SoftwareInfo.asp?ID=23
Free pdf creation programs can be found on the web and may suffice for simple use.