Downright Dunne Right

Suppressing BibTeX fields for specific biblatex entry types

2012-01-12T13:27:00.000-05:00

I use LaTeX for writing academic papers and biblatex for handling the citations and references in them. One problem I ran into is that biblatex prints out the location, address, month, and publisher for a lot of entries, which I prefer not to have in my reference list. Rather than editing the BibTeX .bib file and losing those fields forever, you can tell biblatex to ignore or suppress those fields.

Below is my code. It suppresses location, address, and month for all entries, and suppresses the publisher field unless the entry is a book. You may need to modify this for whatever style you're using.

% Loads biblatex with clickable links from citations and the reference list, 
% with back references if the style supports them.
\usepackage[hyperref,doi,url,backref]{biblatex}
\bibliography{refs.bib}

\AtEveryBibitem{% Clean up the bibtex rather than editing it
 \clearlist{location}
 \clearlist{address}
 \clearlist{month}
 \clearlist{series}
 
 \ifentrytype{book}{}{% Remove publisher except for books
  \clearlist{publisher}
 }
}

Microsoft Security Essentials Automatic Updates

2011-08-08T12:53:00.004-04:00

I love Microsoft Security Essentials, but I'm annoyed by having to do the virus signature updates manually with each Windows Update. This could be because I have Windows Update set to download but let me choose which ones to install. However, you can use the Task Scheduler to automatically run the signature update every day.

AddictiveTips provides instructions, but on my 64-bit Win7 machine the file location was different.

Instead of

C:\Program Files\Microsoft Security Essentials\MpCmdRun.exe SignatureUpdate

I used

"C:\Program Files\Microsoft Security Client\Antimalware\MpCmdRun.exe" SignatureUpdate

So far, so good!

Make Firefox 4 to save passwords for ALL websites

2011-05-31T13:55:00.003-04:00

Some websites ask web browsers to disable their password auto-complete features. This allows developers to increase the password security for important sites like banking, but can also be used for less important sites.

You can force Firefox to ignore the website settings and save all passwords, but you must then be extra vigilant about which passwords you save. Banking sites and the like will now prompt you to save the password, which you probably shouldn't do for them.

There was an easy fix for Firefox before version 4 (see this post), but there are a few hoops to jump through for the latest version. Firefox 4 packages all the necessary files into omni.jar in the program folder, which is a non-standard archive format that needs to be specially altered. Below are the directions from this comment:

0. Make a backup copy of omni.jar
1. Unzip the omni.jar (using either 7zip, Winrar)
2. Edit accordingly
3. Pack again using ZIP format + SFX option (Self-Extract)
4. Rename back to omni.jar
5. Launch Firefox!

Better APA-style: working around hyperref and apacite problems

2011-03-25T12:15:00.010-04:00

I'm writing an article in LaTeX using APA style, so I'm using the popular
apa.cls style. It defaults to using apacite for citations and references, which works well enough.

But if I have a URL field in the BibTeX, like I always do in JabRef to remember where I found things, it prints it for each reference wasting a lot of space and not breaking lines properly. I also like the URLs I do show to be clickable hyperlinks, and my citations and cross-references as well. You can usually do this using hyperref, but a lot of things break when using apacite and hyperref together. Here's the top of the file:

\documentclass[jou]{apa}
\usepackage{hyperref}

And here is the output of pdflatex:

! Undefined control sequence.
\hyper@@link ->\let \Hy@reserved@a 
                                   \relax \@ifnextchar [{\hyper@link@ }{\hyp...
l.83 \cite{Aris09Visual}
...
! Argument of \@@cite has an extra }.
 
                \par 
l.83 \cite{Aris09Visual}
...
Runaway argument?
>{\hyper@link@ }\def \reserved@b {\hyper@link@ [link]}\futurelet \@let@token \E
TC.
! Paragraph ended before \@@cite was complete.
 
                   \par 
l.83 \cite{Aris09Visual}

Other people have had this problem before, but there aren't any great solutions. See the end for a good solution using biblatex-apa instead of apacite. If you insist on using apacite, there are instructions here for how to make things mostly work:

The simplest way to fix the problem is to put a single
instance of \protect into hyperref.sty.

Turn this:
   \def\bibcite#1#2{%
     \@newl at bel{b}{#1\@extra at binfo}{%
       \hyper@@link[cite]{}{cite.#1\@extra at b@citeb}{#2}%
into this:
   \def\bibcite#1#2{%
     \@newl at bel{b}{#1\@extra at binfo}{%
       \protect\hyper@@link[cite]{}{cite.#1\@extra at b@citeb}{#2}%
This occurs at
line 3972 in hyperref.sty [2007/02/07 v6.75r
and at
line 4939 in hyperref.sty [2008/04/05 v6.77l
(line 8328 of the corresponding hyperref.dtx ).

but this breaks the citations. Later they added additional code to the tex file:

It's really just a matter of executing APA's version of \bibcite
before doing the extra stuff that hyperref needs to create the hyper-linking (which seems to work just fine).

For example, the following coding seems to work OK.

\usepackage{apacite}
\let\APAbibcite\bibcite   %%%%  add this line

\usepackage{color}
\definecolor{darkblue}{rgb}{0.0,0.0,0.3}
\usepackage[bookmarks=true]{hyperref}
\hypersetup{
   pdfauthor={Salvatore Enrico Indiogine},
   pdftitle={},
   pdfsubject={TAMU EDCI},
   pdfkeywords={},
   pdfcreator={LaTeX with hyperref package},
   pdfproducer={dvips + ps2pdf},
   colorlinks,breaklinks,
   linkcolor={darkblue},
   urlcolor={darkblue},
   anchorcolor={darkblue},
   citecolor={darkblue}}

%%%%  add the following 2 lines
\let\HYPERbibcite\bibcite
\def\bibcite#1#2{\APAbibcite{#1}{#2}\HYPERbibcite{#1}{#2}}

This fixes most problems, but there are still warnings and ampersands missing in the references.

A better solution for me was to use biblatex-apa with biblatex instead of apacite.

First replace \bibliography{...} at the end of your tex file with \printbibliography. Then modify the the top to look like this (note the noapacite option for apa.cls).

\documentclass[jou,noapacite]{apa} %%%% apacite is buggy with hyperref

\usepackage{color}

\usepackage[]{hyperref}
\hypersetup{
   pdfauthor={AUTHORS},
   pdftitle={TITLE},
   pdfkeywords={KEYWORDS},
   colorlinks,breaklinks,
   linkcolor={blue},
   urlcolor={blue},
   anchorcolor={blue},
   citecolor={blue}}

%%%% bilatex-apa
\usepackage[american]{babel}
\usepackage{csquotes}
\usepackage[style=apa,hyperref,doi,url]{biblatex}
\DeclareLanguageMapping{american}{american-apa}
\bibliography{}

CrashPlan local backup phones home way too much

2011-03-24T14:34:00.002-04:00

I recently tried using CrashPlan, an online backup program that also provides a free client for local or local network backups. I was not happy when I discovered how much it phoned home for these supposedly local backups.

After watching the EFF's presentation The Law of Laptop Search and Seizure from DEFCON 18, I discovered that only a subpoena is required to get your data from an online provider while a court-approved warrant is needed to search your personal machines. CrashPlan claim to use file and network encryption to protect your data on their servers, but I'd much rather roll my own backup servers for the added security.

After installing the CrashPlan proprietary Java client I fired up Wireshark to see how much CrashPlan was phoning home for local backups. When you open the program, you're forced to create an account with their online service, so naturally it sends that info. I was surprised though when I started configuring local backup settings and that information was sent to their servers too. Why do they need all your configuration? To populate their web interface.

This web interface could be useful for users wanting to change their settings remotely, but I'm not pleased with all my backup selections, destination folders, exclude lists, and the like forwarded on to their service and configurable there. It would be easy for them to store a lot more information about the files on the machine without the end user knowing.

CrashPlan seems to provide a good service for users wanting to do online backup, but one of their main selling points is the free local backup system. I'd be much happier with it if they gave an option to switch the web interface and all phoning home off. As it is, I'll stick with my harder to set up but open source and private BackupPC system.

LaTeX Error: Undefined Color when using apa.cls

2011-02-09T12:19:00.007-05:00

I was writing a journal article in LaTeX using the apa.cls style and was having trouble with my little command for leaving notes to myself:

\documentclass[jou]{apa}
\usepackage{color}
...
\definecolor{Orange}{rgb}{1,0.5,0}
\newcommand{\todo}[1]{\textsf{\textcolor{Orange}{[#1]}}}

On building, I'd get an error message: LaTeX Error: Undefined Color `ORANGE'. It only happened when using the jou option, not with man or doc. I couldn't for the life of me figure it out, and on a whim changed the color from Orange to ORANGE. Viola! It works perfectly! Apparently something in there automatically upper-cases the color.

\definecolor{ORANGE}{rgb}{1,0.5,0}%Lowercase breaks on \documentclass[jou]{apa}!
\newcommand{\todo}[1]{\textsf{\textcolor{ORANGE}{[#1]}}}

Full/Incremental Backup Cutoff in Windows 7 Backup

2010-10-29T13:30:00.005-04:00

I couldn't understand why the Windows 7 Backup would sometimes do incremental backups and other times full ones. After much searching, here's what I found on the TechNet Forums:

We have introduced automatic full backup feature in Windows7 to help customers who run into a situation where they never create full backups. When their backup target eventually gets filled, they are left with only one backup set to delete. They need to delete the entire backup set to resume backups and so end up in a situation where they do not have any backup.

The rules that determine when to take automatic full backup are:
1. If previous full backup was taken 1 year back
2. Ratio of size of deleted files + older versions of files in current backup set is 50% or more of the size of the current backup if it were full.

We deliberately did not allow forcibly starting new backup set or configuring these rules through our UI because we did not want to confuse users about full backups, incremental backups, automatic full backups.

If you find that these settings do not match your requirements, we allow the defaults to be tweaked using registry keys.

Registry key to control enable/disable automatic switching to full backup:
Path: SOFTWARE\Microsoft\Windows\CurrentVersion\WindowsBackup\AutomaticFullBackup
Name: Enabled
Type: DWORD
Value: 0 indicates automatic full backup is disabled, non-zero indicates it is enabled
Default if not specified: 1
Registry key to control the time period when backup should automatically switch to full:
Path: SOFTWARE\Microsoft\Windows\CurrentVersion\WindowsBackup\AutomaticFullBackup
Name: TimePeriodInDays
Type: DWORD
Value: Count of days
Default if not specified: 365
Registry key to control the % of deleted/missing + older versions of files that determines whether to switch to full backup:
Path: SOFTWARE\Microsoft\Windows\CurrentVersion\WindowsBackup\AutomaticFullBackup
Name: OlderFilesSizePercentage
Type: DWORD
Value: Percentage value from 0 to 100
Default if not specified: 50

...

A lower value for OlderFilesSizePercentage would mean the automatic full backup would trigger earlier than when it would trigger if this key was not set. Hope that is clear.

To clarify on your question on incremental backups to network storage location:
Windows Backup supports incremental backup to network storage locations. This is true for file backup as well as system image backup.

However in case of system image backup, Windows Backup supports only preserving the latest version of the system image backup. This is because system image backup versions currently are maintained as shadow copy versions of the backup target volume containing the backups. Since shadow copy cannot be created on network shares, it is not possible to support multiple versions of system image when taken to network share.

Example command line usage:

wbadmin start backup -vssfull -backuptarget:y: -include:c:,d:

This would only support taking a block-level backup of the entire volumes included in backup in client SKUs. (That is why if you have noticed, you can only include full volumes as part of "wbadmin start backup"). So this does not end up creating a new backup 'period' for the file backups.

Use empty string instead of zeros for failed VLOOKUP

2010-05-12T16:37:00.008-04:00

When using VLOOKUP in Excel/NodeXL, you may often get zeros when looking for text and it isn't found. In many cases you may want an empty string instead. For example

=VLOOKUP([@[Vertex 2]],Vertices,COLUMN(Vertices[Flags]),FALSE)

returns 0 when the Flags column for Vertex 2 in the Vertices worksheet is empty. Our tools work better with empty cells. So rather than write something gross like

=IF(VLOOKUP([@[Vertex 2]],Vertices,COLUMN(Vertices[Flags]),FALSE)=0,"",VLOOKUP([@[Vertex 2]],Vertices,COLUMN(Vertices[Flags]),FALSE))

that does the search twice, just use the T function that automatically turns it into text.

=T(VLOOKUP([@[Vertex 2]],Vertices,COLUMN(Vertices[Flags]),FALSE))

Better vlookup for edges in NodeXL

2010-05-12T16:36:00.006-04:00

I recently was using NodeXL and had to use VLOOKUP to copy vertex info over to the edge worksheet. Rather than having to deal with obtuse indexes and the like you can refer to the columns and worksheets by name. For example, instead of something like this as your formula

=VLOOKUP(A3,Vertices!1:1048576,29,FALSE)

you can use this instead

=VLOOKUP([@[Vertex 1]],Vertices,COLUMN(Vertices[Pub Year]),FALSE)

This uses NodeXL's named worksheets and columns instead. Also, counting offsets can get pretty tedious, especially with how NodeXL hides columns and how many of them there are. By using the COLUMN function you don't have to!

Importing BibTeX into Endnote

2009-09-16T11:46:00.006-04:00

I recently downloaded a trial for Endnote, a proprietary reference manager. I wouldn't recommend it, especially for the price as free open-source alternatives like JabRef do a much better job at no cost. That, and I use LaTeX with BibTeX for my papers, and JabRef works much better with that. Another option that is more LaTeX friendly is the Mendeley beta. It looks better than JabRef, but doesn't have all the functionality and is definitely beta. The built-in pdf viewer isn't to good, either.

However, if you need to get references from BibTeX into Endnote, you can easily use JabRef to do so. First, open your .bib file in JabRef. Then, go to File->Export and select RIS (*.ris) as the file type. Save the export, then open up Endnote. Go to File->Import and choose the saved export. Pick Reference Manager (RIS) for the import options and hit Import. Viola!

Network of Connected Risk Countries

2009-07-13T16:36:00.007-04:00

Here's a new visualization I created of the network of connected countries in the strategy game Risk, colored by node and edge betweenness centrality. You can easily see that Africa and Europe (the connected blob in the center) are harder to hold. Also, the Middle East, part of Asia in the game, belongs more with Europe and Africa according to Newman's community finding heuristic.

The picture was drawn in SocialAction. Below are the data files (based on the adjacency matrix from Yura.net Domination) in
HCIL Network Visualization Input Data Format:

BackupPC Install Guide for Windows XP/Vista Clients

2008-11-03T21:17:00.004-05:00

I've been working on getting BackupPC set up on my home network, and as part of that process I've kept notes of everything I had to do (twice, now). I rewrote them as the BackupPC Install Guide for Windows XP/Vista Clients available on my UMD CS site.

To backup Windows clients, I used Cygwin, rsyncd, and a pre-established SSH tunnel because of problems with regular rsync over SSH when using Windows and BackupPC.

rsyncd exclusions for using BackupPC on Vista

2008-09-29T00:45:00.017-04:00

Edit: These exclusions have expanded/corrected and are further detailed in my BackupPC Install Guide for Windows XP/Vista Clients.

I've been working on getting BackupPC set up on my home network. To backup Windows clients, we've had to use cygwin+rsync+ssh. Because of problems with that combination on Windows, I used rsyncd instead of just rsync over ssh.

When I finally got that working, I ran into a lot of problems on my Vista machines where rsync would follow the junction points they added for backward compatability (see this site for more info). This caused extra-long filenames rsync couldn't handle. To find all junction points on your Vista machine use this command at the C: drive in the Command Prompt:

dir /a /l /s > c:\users\USERNAME\JunctionPoints.txt

So I had to add all of these to the exclude list for rsyncd. Here is my rsyncd.conf (with redacted data, of course):

gid = users
read only = true
use chroot = false
transfer logging = false
log file = /var/log/rsyncd.log
log format = %h %o %f %l %b
hosts allow = BACKUPPC_IP
hosts deny = 0.0.0.0/0
auth users = BACKUPPC_USERNAME
secrets file = /etc/rsyncd.secrets
strict modes = false
[c]
path = /cygdrive/c
exclude from = /etc/exclude-c.txt

The 'exclude from' line specifies the location of the exclude file. Below are the contents of exclude-c.txt for the junction points:

#Junction points
- /Users/All Users
- /Users/Users/Default User
- /Users/Users/All Users/Application Data
- /Users/Users/All Users/Desktop
- /Users/All Users/Documents
- /Users/All Users/Favorites
- /Users/All Users/Start Menu
- /Users/All Users/Templates
- /Users/Public/Documents/My Music
- /Users/Public/Documents/My Pictures
- /Users/Public/Documents/My Videos
#Excludes these junction points common to every user profile
- /Users/*/Application Data
- /Users/*/Cookies
- /Users/*/Local Settings
- /Users/*/My Documents
- /Users/*/NetHood
- /Users/*/PrintHood
- /Users/*/Recent
- /Users/*/SendTo
- /Users/*/Start Menu
- /Users/*/Templates
- /Users/*/AppData/Local/Application Data
- /Users/*/AppData/Local/History
- /Users/*/AppData/Local/Temporary Internet Files
- /Users/*/Documents/My Music
- /Users/*/Documents/My Pictures
- /Users/*/Documents/My Videos

The rules with asterisks in them will match the junction points that are in every user profile by default without having to code each user manually.

Then, to get rid of any temp data in the backups we use the following:

- /Users/*/AppData/Local/Microsoft/Windows/Temporary Internet Files
- /Users/*/AppData/Local/Temp
- /Users/*/NTUSER.DAT
- /Users/*/ntuser.dat.LOG1
- /Users/*/ntuser.dat.LOG2
- /Users/*/AppData/Local/Microsoft/Windows/UsrClass.dat
- /Users/*/AppData/Local/Microsoft/Windows/UsrClass.dat.LOG1
- /Users/*/AppData/Local/Microsoft/Windows/UsrClass.dat.LOG2
- /Users/*/AppData/Local/Microsoft/Windows Defender/FileTracker
- /Users/*/AppData/Local/Mozilla/Firefox/Profiles/*/Cache
- /Users/*/AppData/Roaming/Microsoft/Windows/Recent
- *.lock

Finally, any program or system installation files can be omitted. On Vista, only original installation data is stored in Program Files. Any data programs write to their installation folder goes to ProgramData automatically instead. The Windows folder shouldn't hold anything interesting, either. The rest of these rules are replaceable or unimportant data:

- /Program Files
- /Windows
- /$Recycle.Bin
- /MSOCache
- /System Volume Information
- /autoexec.bat
- /bootmgr
- /BOOTSECT.BAK
- /config.sys
- /hiberfil.sys
- /pagefile.sys

If you're only backing up the users folder, you can omit the last rules and remove the '/Users' prefix from the rest of the rules.

And viola! Finally we can get a full backup!

NetGrok released

2008-09-28T02:04:00.002-04:00

We've finally released our Information Visualization class project NetGrok, which is a tool for visualizing computer networks in real-time. Our paper for it was published as part of the proceedings of VizSEC 2008. Read more at the project site check out the source at Google Code.