Defindit Docs and Howto Home

This page last modified: Feb 06 2013

535 smtp auth fix

Fixing a 535 smtp auth failed error in Gmail

Actiontec Dual PC external narrowband 56K modem is an ethernet router

The Actiontec Dual PC modem is really an ethernet router with a built-in 56K modem.


Analog report tutorial

A quick overview on how to interpret web site traffic reports from Analog.

Apache allow/deny and OSX

Why allow/deny directives may not work with Apache and OSX.

Apache certificate notes

Apache Explanation of (13)Permission denied: cannot read directory for multi:

When permissions are NOT the problem, a common cause of the 13 error explained.

Apache httpd Phusion mod_passenger Ruby Rails

Configuration for the Phusion passenger gem and Apache module with Rails coexisting with normal HTML web pages and Perl CGI. Also some notes about running Ruby on Rails with CentOS 5.

Apache httpd suExec, Rewrite and VirtualHost

How to get suExec working for Virtual Hosts and RewriteEngine examples for scripts.

Apache logging and favicon.ico

Workarounds and suggestions for not logging requests for favicon.ico.



Bash info, scripting examples, regex parameter substitution, interactive shell, and more

Shell trivia and scripting examples including file name and path substitutions, as well as how to detect a live human logging in, and how to fix the session title and titlebar.

bash sh shell io file descriptor redirection (applies to cron too)


BLAST "Failed to allocate" error

Cause and workaround for NCBI BLAST "Failed to allocate" error.

Camcorder feature list and video hints

Hints about choosing a quality consumer digital camcorder, and creating good movies.

Camtasia lock up work around.

Prevent Camtasia from hanging with large presentations.



Checking logical volumns with e2fsck and hints for smartd

How to make a logical volume active and check for bad blocks with fsck (e2fsck), how to run smartd, how to find alternate superblocks.


Common Unix Printing System notes

Hints and configuration for CUPS


CVS setup and configuration

Setting up and using a CVS version control repository.

Daemons: Fedora, Linux list of daemons with descriptions

Full list of all Fedora Core 3 daemons, with their recommended state and a description of each.




Dual-head X Windows nVidia configuration

Fedora 8 working dual-head TwinView X Windows nVidia with different size monitors.

Emacs and .Xdefaults, Mule set, Mule save

Getting emacs to start faster with a different font as well as setting and saving a Mule font.

Emacs configuration and remote file access examples

Hints on setting up your emacs configuration, and remote file access.

Emacs hints, GPG, pgg-decrypt, include lines, paste, unfill

Emacs GPG, pgg-encrypt, ansi-term, cursor logical move, paste at cursor, unfill paragraph

Emacs key commands for beginners

Quick notes on how to learn and use Emacs in less than five minutes.

Emacs lisp increment variable macro (the hard way)

Emacs toggle hide show menu and tool bars

How to hide or show Emacs menus and toolbars.





Ethernet setup and problem solving with Linux and Fedora

Example of working firewall and local area network with a private ethernet subnet. Includes some problems you may encounter, and how to diagnose them.


Examples of Linux checksum fingerprints for files: md5, sha.

How to get checksum fingerprints

Exmaples and tricks using the Linux (Unix, OSX) "find" command.

Arbitrary dates and other tricks with the Linux find command.

Fasta files converted to NCBI BLAST search libraries with formatdb.

The NCBI formatdb silently changes accession numbers if the numbers don't conform to a certain convention.

Fedora KDE X Fonts install setup config mini howto

Change window defaults (border, title) with KDE, useful settings, XMMS, Emacs fonts, X-windows fonts, and Firefox fonts.

Fedora sound notes

Setup sound for Fedora 8 with pulseaudio and ALSA.


Firefox disable Evolution enable Thunderbird KDE

KDE settings can be overridden by Gnome gconfd values. This shows how to find them and fix the problem.

Firefox maximize windows fullscreen and config

How to default firefox to full screen maximized windows, and how to use the about:config interface with KDE. Link to Firefox font config.

Gbrowse installation notes

Fedora 11 additional dependencies for the network install of GMOD Gbrowse.

gconfd error fix and mini howto

Diagnosing and solving a small configuration problem with KDE and gconfd.



GPG use notes.

GSS search and protein aligment explained for programmers.

How to verify translation between Blastx results and an original gene space sequence.

Hints about MPlayer codecs and streaming problems

Hints about MPlayer especially streaming Quicktime video.

Hints, tricks and suggestions for Google Docs spreadsheets and documents.

A quick tutorial on Google Docs spreadsheets import and hits about documents.

How to run SPC ISB tools.

How to run readw.exe, msxml2other.exe, dtafilter, sequest27.exe, out2summary, interact.

How to shoot better movies

Recommendations to make your home movies and video more professional

HTML::Template notes and hints

Examples of Perl and HTML for using the HTML::Template Perl module

HTTP header examples

Examples of content headers for web pages and downloads




Installing Flow LIMS

Installing xemacs, xemacs highlight (hilite) zmacs-regions

Installing xemacs, xemacs highlight (hilite) zmacs-regions

Intel Pro 1000MT NIC in Dell Poweredge 700 server

Fedora Core 1 has bad drivers for the Intel Pro 1000 series ethernet on Dell Poweredge 700 servers

iptables configuration and examples for Fedora and Linux

Configuration examples for iptables firewall, including allowing connections, and building a router.


KDE K Menu Start Menu kdemenuedit Menu Editor Fails Launch Problem

Howto fix a small KDE bug where right-click on the K Menu and selecting Menu Edit does nothing.

Konsole menu disable

How to disable the ALT key in Konsole

Kudzu conflicts

Early Fedora Core (3, 5, 8?) have kudzu problems.

LDAP, Tom's mini howto

Tom's mini howto and notes about setting up LDAP

Linux and emacs getting started hints

Linux beginner secrets explained.

Linux command line introduction and examples.

Examples of common commands in Linux shells and how to use the command line.

Linux features and problems

My constantly growing list of problems one encounters when running Linux on the desktop. Includes some strenths, but is mostly about opportunities for improvement.

Linux vnc server with Apple Macintosh OSX screen sharing client

Notes about installaiton, set up, and configuration for tigervnc and x11vnc on Fedora 14

Localization and internationalization settings for sorting and collating.

Logging hints for SMART and smartd

Remove extra, false log messages created by smartd.


Mac OSX bash del broken with ^[3~

How the keypad Delete key is broken with OSX bash.


Manual install of Google Chromium Linux.

Steps to install Google Chrome unstable .deb on Fedora

miRBase mirna converted to SQLite

A Perl script and instructions to convert the miRBase schema definition file from MySQL to SQLite and load the data.


MS Windows recovery options

Acer, Toshiba, and Dell options for operating system recovery.

MySQL notes

Hints and notes for getting started with MySQL

NCBI file extensions

A brief description of file extensions and file formats found at the National Center for Biotechnology Information

NDT client build and test

Build the web100clt from source, and run to determine network speeds.




Nokogiri Builder examples.

Working code examples for adding a child node to a Nokogiri Builder object.

Notes about transcoding flac and ogg music files

Brief notes on transcoding flac to ogg or faac.

OMSSA Hints and Howto

How to choose and determine options for OMSSA and omssacl


OSX hints and info

Tom's OSX hints for Linux users

OSX isses and hints

An honest list of Apple Computer OSX problems


PBS setup configuration debugging

Configuration suggestions and diagnosing problems with the Portable Batch System PBS (e.g. OpenPBS).

Perl module minimum requirements

Perl module examples, including a tiny module and Perl scripts.

Perl one liners

Perl one line scripts run from the command line or used in piped commands in the shell.

Perl profiler

Perl SQL example using DBI/DBD and HTML::Template

Working examples of Perl DBI code reading and updating a PostgreSQL database and displaying the results in a web page.




pgdump notes


PLPerl Notes

Brief notes about Perl inside PostgreSQL

Portable buttons in CSS

How to create pure CSS buttons that work with Firefox and Internet Explorer

PostgreSQL command line psql, SQL tricks, pg_hba.conf configuration

Examples of PostgreSQL commands run from the shell, and some advanced SQL queries. Also an install/upgrade checklist, and pg_hba.conf configuration examples. Includes info about the DBD/Pg error message.

prelink and tripwire

Cron daily runs prelink which modifies executables to make them load faster. This changes the file sizes and tripwire returns a warning.

Quick numbered backups using cp

Use cp to quickly great numbered backup files

Rails CGI HTTP variables

How to access CGI environment variables from Ruby applications running under Rails.


RCS Keywords, date, etc. and timezone hints

Keyword variables available in RCS, and how to force the timezone to be local.

Rebuild an rpm database when rpm (and yum) hang.

What to do when yum hangs because rpm is hanging.

RPM use notes.

Rsync explanation and recommendations

An explanation of how rsync manages directories, and recommended usages with examples.






SQLite as data file format

Why SQLite is the best format for data files and warehousing.

SQLite example for beginners

Sample session transcript of running SQLIte version 3, creating a table, inserting record, and selecting records.

SQLite from MySQL and AmiGO Gene Ontology

A Perl script and instructions to convert MySQL to SQlite using the AmiGO Gene Ontology database as an example.

SQLite hints and Perl DBI mini-howto.

Speed hints, examples SQLite commands, and Perl DBI/DBD examples.

SSH public key authentication including scp, sftp, sshfs and X11 forwarding

Configuring ssh to use your public key, scp notes as well as SELinux context problem diagnosis and fixes, sshfs and fuse, and how to configure X11 forwarding in order to run Firefox and Emacs in graphical mode.



Tar (tape archive) examples

Examples using tar to create multiple smallers files (volumes).

Thunderbird password reset

Reset and clear the master password for Thunderbird email


Tom Laudeman's .emacs file aka dot emacs file

Example emacs configuration file with extensive comments and elisp functions.

Tufts TAPER SABT install

Installing and configuring the original Tufts TAPER Submission Agreement Builder Tool


unrar and rar install via yum

Install unrar or other rar support packages on Fedora 11 or Fedora 12 (or any other Fedora distro)

Upgrading Fedora versions using yum and rpm and preupgrade

Upgrade from Fedora 10 to Fedora 11 via yum and a network update.


Using ntpdate to easily keep clock correct

Using split and cat to help edit large files.


Webmin setup and config with Fedora

Notes for getting webmin working with Fedora.



Working iPod with Fedora 8, PulseAudio, XMMS, gtkpod

Working iPod Nano configuration with Fedora 8

X11 hints, xterm, also with hints for Icewm on Apple MacOS

Installation, configuration and hints X-windows, xterm, for Icewm window

XFCE setup and tips

Some hints for working with the XFCE desktop windowing system.


XSLT Hints and examples

Sample XSLT scripts

Yum GPG keys: Find and Install keys for Fedora Linux

Yum command line hints (all versions of yum) and how to install yum GPG keys (especially Fedora Core 3 Linux).

Zonet ZFM5600-CF PCMCIA modem works great with Fedora Core 3 Linux.

Zonet ZFM5600-CF PCMCIA modem works great and appears to be totally compatible with Fedora Core 3 Linux.