Category Archives: Computers

Changing the LibreOffice bibliography database

Goal: replace or update the default bibio database in LibreOffice with a user defined database.

For citations and building a bibliography in LibreOffice Write, please see this previous post

  1. Find the default bibiography database. On my Mac, the LibreOffice bibliography database, biblio.odb, is located at [username]/Library/Application Support/LibreOffice/4/user/database/
  2. rename the file, e.g., default_biblio.odb
  3. Export database from JabRef. I tried several options, the best results I had was saving the database as sxc spreadsheet, the LibreOffice format.
  4. Import the spreadsheet file into LibreOffice Base and save as a odb database.
  5. File → New → Database
  6. which brings up the Database Wizard. Select Connect to an existing database, and select “Spreadsheet” from the drop-down menu.
  7. Click “Next” to continue. Browse to find the spreadsheet file, then press Next again. Accept the defaults (Yes, register the database for me, Open the database for editing), and click Finish to save the database.
  8. LibreOffice Base will open and display your references. Make changes as needed. Then quit base and proceed to connect the exported database so that it will
  9. LibreOffice → Preferences→ LibreOffice→ Base→ Databases.
  10. Click on “New” and browse to the location of your saved bibliography.
  11. Then, update the entry in Registered name so that it reads “Bibliography”
  12. Click OK. If all goes well, when you access references in LibreOffice Write via the Tools → Bibliography database command, then your bibliography will be present.

JabRef citations and bibliography in LibreOffice

This post is about citations and bibliography in LibreOffice Write. For citations in Word, see this post. For instructions for updating the bibliography database in LibreOffice, see this post.

JabRef (ver 3.8.2) & LibreOffice Write (version 5.3.3.2)

This method uses the jabref plugin for OpenOffice/LibreOffice Write

  1. Must start java. LibreOffice → Preferences → Advanced. Provided you have a runtime environment installed (JRE), it will show in the popup window. Simply click on the button, then OK to save the changes. Restart LibreOffice before proceeding.
  2. Start LibreOffice and write your manuscript. Keep your document in the odt format native to LibreOffice.
  3. Return to Jabref, start the OpenOffice/LibreOffice connection: Tools → OpenOffice/LiberOffice connection. The tool will appear along the left-hand side.
  4. Next, connect JabRef to your LibreOffice app. There are two options: Automatic and Manual. I’ve yet to get the automatic option to work, so Manual it is. Click on the Manual icon (second from left). A window pops up, enter the path to your installation of the LibreOffice Mac. On my computer, that would be /Applications/LibreOffice.app. Click OK. View status of the connection at the bottom-left of the JabRef GUI.
  5. If all goes well, you’ll get a prompt to select the LibreOffice document. You can also select the document via the darkened folder icon (third from left). Status of the connection is reported bottom-left of the JabRef screen.
  6. Now, insert a citation by placing the cursor in text and then switching to JabRef.

Highlight the reference in JabRef, then click on the Cite button. Here’s what you should get

Report on ozone and toad innate immune function [Dohm et al. 2005]

  1. To generate the Bibliography, place cursor where you want the item to appear in the document, then switch back to JabRef.
  2. Highlight the reference, or references, then click on the refresh button (fourth from left). Here’s what a single reference will look like

References

Dohm, M. R.; Mautz, W. J.; Andrade, J. A.; Gellert, K. S.; Salas-Ferguson, L. J.; Nicolaisen, N. and Fujie, N. (2005). Effects of ozone exposure on non-specific phagocytic capacity of pulmonary macrophages from an amphibian, Bufo marinus, Environmental Toxicology and Chemistry 24 : 205-210.

Using LibreOffice Bibliography database

  1. Assuming you have incorporated your own references into the database (see this post for instructions), then select Insert → Table of contents and index → Bibliography Entry. A popup window will appear from which you select your citation from your bibliography database.
  2. Click insert and then close to return to your manuscript. If all goes well, then you will see

Type something here [Adams2008]

  1. To generate the bibliography for the paper, select Insert → Table of contents and index → Table of Contents, Index, or Bibliography. A pop up menu appears.
  2. Select “Bibliography” from the type drop down menu. At least to start, accept the defaults and press the “OK” button. If all goes well, then you’ll see

Bibliography

Adams2008: Adams, Dean C., Phylogenetic meta-analysis, 2008

[note — need to fix my database!]

Papers3 + LibreOffice

  1. As described in a previous post, just press the ctrl key twice in succession to bring up a citation manager. Instructions as before. Here’s the output

The citations in text:

A paper about social networks and scientists {Hall:2014db}

Another paper, introducing Richard Hammond’s address to a Bell Research seminar group {Erren:2007hl}

  1. And the bibliography, as described in the previous post

Erren, T. C. (2007). Ten simple rules for doing your best research, according to Hamming. PLoS Computational Biology, 3(10), 1839. http://doi.org/10.1371/journal.pcbi.0030213

Hall, N. (2014). The Kardashian index: a measure of discrepant social media profile for scientists. Genome Biology, 15(7), 424. http://doi.org/10.1186/s13059-014-0424-0

Explore and compare working with JabRef, Papers3, and Word 2008

Over the years I’ve built up a large reference list. The list has now more than 5000 entries, which reflects

  • I’m getting old: I remember when Pubmed became available to everyone over the Internet (1997) and Google Scholar appeared in (2004).
  • It’s important to my teaching style to be able to present students with access to the papers used in my lectures.
  • I like to teach my courses (biostatistics, genetics, etc.,) from a perspective of historical context.
  • My research interests have changed.

I initially managed the list with the first version of EndNote, continuing through EndNote2 through EndNote5, then a few years with the excellent and free to use Mendeley until I reached their 2GB limit on the free account. I would have continued to use Mendeley but for their choice of subscription pricing as opposed to my preference for a purchase of a onetime license. That said, I settled on JabRef and have used it for years.  As a reference database, JabRef is tops in my book, plus it’s Open Source and cross-platform software. It’s less convenient working with manuscripts when you want to cite and build a bibliography, but it certainly works. JabRef works better with LibreOffice documents than Microsoft Office documents (see this post), but it can work with Word if you use Word’s bibiliography functions and with a little run-around. Since I’ve recently become interested in Papers, thought I’d share my notes as I go.

In this posting I present brief instructions for adding citations and a bibliography to a Word 2008 document with combinations of JabRef and or Paper3.

JabRef (ver 3.8.2) & Papers3

Goal: Import selected reference list into Papers3 from JabRef

  1. From JabRef, select one or more references. File→ Save selected as… to BibTex *.bib database.
  2. Start Papers3
  3. File→ Import→ BibTex library

Note: Papers3 will import my entire JabRef database, but that’s unnecessary for the example.

Papers3 + Word 2008

Goal: cite as you type; append bibliography to manuscript

  1. Type away in Word 2008
  2. When ready to insert a citation(s), press the control key twice. This brings up a Papers3 Search window. Notably, Papers3 does not have to be running.
  3. Enter relevant search word(s) and papers will show up in the results window. Among the nice features of Papers3, you can view the article.
  4. Click on Insert Citation, and it returns back to Word 2008
And here’s what it would look like in the Word document:

Here’s a citation of a Phylogenetics book {Adams, 2008}. Here’s a citation of an article on women in statistics {Anderson, 1992}.

  1. Once you are finished adding in citations, generate the bibliography by invoking the Papers3 search again (ctrl+ctrl), then select “Format manuscript” (Appendix).
  2. Nice to know: This method works  with the free Word Online — since you would need a full install of  Word/Office in order to insert citations and generate a bibliography, use of Papers3 may be a nice alternative. The method also works with Google Docs; again, there are options to gain this type of function in Google Docs, but they are either limited or cost (e.g., free version of EasyBib Add-on has very limited function).

JabRef + Word 2008

  1. From JabRef, select multiple papers. Export selected entries and save file as Sources.xml to Documents → Microsoft User Data
  2. Start Word 2008
  3. Type away.
  4. When ready to insert citation, bring up Citations Toolbox (View→ Toolbox→ Citations)
  5. Click on the Settings icon (bottom right of popup menu); Select Citation Source Manager
  6. If all is well, you will see the sources listed in the Master List panel. Select the references required and copy them to the Current List panel. Hold down Command key to select multiple references.

And here’s what it would look like in the Word document:

Here’s a citation of a Phylogenetics book (Adams, 2008). Here’s a citation of an article on women in statistics (Anderson, 1992).

  1. Once you are finished adding in citations, generate the bibliography by placing the cursor in the document where you want the bibliography to appear (e.g., end of document), then select from the menu bar: Insert → Document Elements→ Bibliography (Appendix).

Conclusion

Much easier to use Papers3 and Word 2008 together, although the results are pretty much the same. Frankly, if this was all you are looking to do with Papers, then probably not worth the additional cost. (However, Papers can do a lot more; I particularly like how it helps you manage all kinds of documents on your computer).

Appendix

Output from Word 2008, Insert → Document Elements→ Bibliography

Bibliography

Adams, D. C. (2008). Phylogenetic meta-analysis. Evolution , 62, 567-572.

Anderson, M. (1992). The history of women and the history of statistics. Journal of Women’s History , 4.

Output from Papers3, “Format manuscript”

Adams, D. C. (2008). Phylogenetic meta-analysis. Evolution, 62, 567–572.

Anderson, M. (1992). The history of women and the history of statistics. Journal of Women’s History, 4(1).

 

How to install R on Windows 10 PC

  1. Go to https://cran.r-project.org/
  2. Select Download R for Windows
  3. Select “base” and then click on “Download R 3.4.0 for Windows” to get the latest version. As of June 2017 that would be

R-3.4.0

  1. Download the file; once completed, click on the file to begin installation. Accept defaults.
  2. After R has been installed, start the application to work with the R statistical software.

Next: How to install Rcmdr and other R packages

How to install R on your Mac

You must install XQuartz, an X windowing system, before you install R.

Install XQuartz on your Mac

  1. Got to https://www.xquartz.org/
  2. Select the latest version. As of June 2017 that would be

XQuartz-2.7.11.dmg

  1. Download the file; once completed, click on the file to begin installation. Accept defaults.
  2. If your computer replies with a warning message about installing from unknown sources, you’ve run into “Gatekeeper.” Click here for help with Gatekeeper.
  3. After XQuartz has been installed, it is good practice to restart your computer before proceeding.
  4. Now you can install R.

Note: After updating the operating system, it is recommended that you reinstall XQuartz.

Here’s what Apple has to say about why you need to install XQuartz.

Install R on your Mac

  1. Go to https://cran.r-project.org/
  2. Select Download R for (Mac) OS X
  3. Select the latest version. As of June 2017 that would be

R-3.4.0.pkg

  1. Download the file; once completed, click on the file to begin installation. Accept defaults.
  2. If your computer replies with a warning message about installing from unknown sources, you’ve run into “Gatekeeper.” Click here for help with Gatekeeper.
  3. After R has been installed, start the application to work with the R statistical software.

Next: How to install Rcmdr and other R packages

 

My computer is running really slow after loading a new application

I’ve found that many students are hesitant to load software, with fears based on lack of knowledge about how to install software right up to the very sensible concern about the safety and integrity of software downloaded from websites they have never heard about. I’ll post at a later time on how I instruct students about checksum and other aspects of verifying software. A quick Google search finds all kind of advice on such things. Instead, in this post I wanted to address another interesting aspect of student’s knowledge about their own computers — how to manage the software bloat that comes with new computers and the pre-installed applications.

After installing one or more of these recommended applications I often get complaints from students about how slow their computers have become. Naturally they connect the two — my software slowed their computer. A reasonable conclusion, but not true. While some statistical or bioinformatics routines will tax your personal computer, most of what we will run do not — we run statistics on projects with sample size in the 100s and variables in the range of dozens. Even when we run nonlinear estimation routines or matrix manipulations, these procedures are completed in seconds. Similarly, while sequence alignment and other manipulations potentially can tax a computer, the kinds of work we do in these classes rarely will hang a computer for more than a minute or two.

With this as a backdrop, here’s the advise and help I give students.

Assuming you downloaded the software from the appropriate source and checked it against your anti-virus software, the problem of a slow computer is probably not due to the software you just installed. Poor computer performance is more likely because of the number of processes running on your computer.

On Macs you can check for active processes with Activity Monitor (Applications → Utilities folder); on Windows machines use the Task Manager and select Services. Activity Monitor provides an extensive look at your computer, Task Manager less so, but both can be used to stop processes and thus free up system CPU and memory — and make your computer run faster! Some caution here — do a little Google work to look up process names and confirm that you can indeed stop the process without harming your computer.

Manage Gatekeeper on Mac OS X Sierra

Pertains to Mac OS X 10.12+ (Sierra)

To add “Anywhere” option back to Gatekeeper, open Terminal and at the prompt type

sudo spctl –master-disable

To return Gatekeeper to Sierra default, open terminal and type at the prompt

sudo spctl –master-enable

Note that you will still get the warning quarantine message “[app] is an application downloaded from the Internet. Are you sure you want to open it?

To disable this message, type in Terminal:

defaults write com.apple.LaunchServices LSQuarantine -bool NO

then, restart Finder. Two options

Command+Option+Escape, then select Finder and click on Restart
alternatively, in Terminal type: killall Finder
To enable LSQuarantine, type in Terminal:

defaults write com.apple.LaunchServices LSQuarantine -bool YES

then, restart Finder.

And it should go without saying — use these instructions at your own peril. Apple has very good reasons for incorporating these and other security defaults. Bypassing

source: man sudo; man spctl; osXdaily;

/MD

Change screenshot capture folder on a Mac

To capture screenshots on Macs, shift + command + 4 will allow you to capture a portion of your screen

The default location to save screen shots is the Desktop. To change to a different folder, follow the instructions provided at https://discussions.apple.com/docs/DOC-9081

For example, change from teh desktop to a subfolder created in Pictures. Create the new folder first, then open Terminal. At the prompt, type

defaults write com.apple.screencapture location ~/Pictures/Screenshots/

Press Return to carry out the command.

After the work is completed and a new prompt is displayed, enter

killall SystemUIServer

and press Return key to run the command.

 

Confirmed on Mac 10.12.2

Fix MacBook connect to external projector problem

Problem: MacBook Pro 2010 (MAC OS X 10.11.3) failed to find external VGA projector

Solution: reset SMC (System Management Controller) and PRAM (Parameter RAM)

troubleshooting steps:

Confirmed that the problem wasn’t with mini DisplayPort to VGA adapter (Amazon MB572Z) or with the KanexPro HT201295 Presentation Switcher & Scaler
Shut down the laptop
Discconect the internal battery
Connect laptop to MagSafe 60W power adapter.
To reset the SMC, press and hold left shift + command + option keys plus power button and wait for powerup.
Shut down the laptop again.
Press the power button and listen for the startup chime
To reset the PRAM, immediately before the gray screen appears, press adn hold the left command + option + P + R keys.
Release the keys once the second startup chime is audible.
Hat tip to www.douglane.net, with the following modifications. Because my laptop is Intel-based, then SMC and not PMU applies; second, because my MacBook has a removable battery, I removed it prior to following the instructions at Apple Support document HT201295.

/MD

Uninstalling applications on Macs

Computers come today with lots of pre-installed software, some of which you will use and depend on, others you rarely if ever use. Overtime, and after repeated visits to web sites, after unexplained crashes, etcetera, it may be time to manage the software bloat.

On PCs, use Task manager, on Macs, use Activity Monitor to learn about software processes that are running — check to see of you ever use the associated applications. If you do not, go ahead and uninstall the application.

Windows users know about the Control Panel and running the uninstall option for Programs and applications. This works pretty well, but still may leave some application data scattered at locations on your hard drive that you may want to track down.

However, this post is directed at my Mac-using-students. Mac users may know about dragging applications to the Trash, they may be unaware that this removes none of the libraries that may be installed to support the application. To perform a clean uninstall, users should load and run something like Appcleaner.