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University
of Washington School
of Medicine, Department
of Microbiology
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Computational Biology Group (CBG) performs a two-fold function
in the Mullins Lab: support and research. The CBG administers
the Mullins Lab computer network, and also provides technical
support. Technical support mainly consists training of lab
personnel in software, and assisting them with specific software
and hardware questions should the need arise. More importantly,
the CBG researches and develops computational methods for
the analysis of molecular variation in immunodeficiency viruses.
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Web tools |
- QUALITY
A program that is a variant of the Minimum χ2 (MC) method for limiting dilution assays. It allows the user to specify the probabilities of a false negative and false positive PCR (it is also a tool for the quantitation of ampliable viral templates, i.e., viral load under the conditions of your assay). The program is available either as a java applet that can be run via the web or as a program that can be downloaded and run locally.
- PSSM
A scoring tool developed by Mark Jensen and other lab members that allows users to analyze V3 loop coreceptor motifs.
- ViroBLAST
A BLAST web server that allows users to search multiple sequence databases including public and local.
- DiverAnalysis
A web interface to analyze sequence divergence and diversity.
- EpitopeDB
A web database to store, retrieve and analyze HIV immunology data (ELISpot, HLA, etc.).
- PrimerDB
A web database to store, search and retrieve PCR and sequencing primers specific to HIV (collection from Mullins lab).
- LiteraTracker
A web service to track scientific literature.
- COTree
A web interface that re-roots a newick tree at the least squares point (COT).
- DistParser
A tool to extract branch lengths from newick trees. It returns divergence and diversity values.
- JitterCalc
An Excel spreadsheet that jitters points with identical (x, y) values, i.e., it allows a user to jitter data symbols along the X-axis so that the symbols no longer completely overlap.
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Perl scripts |
- DiverAnalysis.pl
A program to perform phylogenetic analysis of sequence divergence and diversity.
- AutoSequin.pl
A program to speed the process of submitting HIV sequences to GenBank via NCBI's Sequin program.
- NetNGlycParser.pl
A program to parse the output of NetNGlyc 1.0 Server that predicts N-Glycosylation sites
- NetOGlycParser.pl
A program to parse the output of NetOGlyc 3.1 Server that produces neural network predictions of mucin type GalNAc O-glycosylation sites
- ChangeNewickNodeId.pl
A program that manipulates a newick tree by replacing the tree node identifiers with new identifiers that are defined in a file.
- CountAAFreq.pl
A program to calculate amino acid frequencies at each position of a set of aligned amino acid sequences.
- RemoveOverlapSeq.pl
A program to check a set of sequences and remove identical sequences and overlapped short sequences.
- SequLocatorParser.pl
A program to parse the output of LANL's HIV/SIV Sequence Locator Tool
- Sequence manipulator
A collection of sequence manipulating scripts, including sequence cleaning and sequence format conversion.
- List2Fasta.pl
- Nexus2Fasta.pl
- ASN2Fasta.pl
- SwissProt2Fasta.pl
- SequCleaner.pl
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SMS2 |
- (a local port of Paul Stothard's Sequence Manipulation Package)
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Array Analysis Tools
by Daniel Westreich |
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Daniel Westreich, a former employee at the Mullins Lab,
provided an important contribution to the lab through his Perl
programming ability. For more information on Perl scripts used in
Array analysis, please click here
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| University Computing Resources |
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The University of Washington provides a wide array of computing resources and services including:
- Assistance with University Email accounts, also called UW NetIDs
- Campus Labs, including printing centers
- Helpful documents on a wide range of topics
- Site licenses for many kinds of software
- And other resources...
The first place to look for help is at the UW Computing Page
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| The UWICK Kit, University Software for FREE! |
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The UWICK Kit, provided by the University of Washington, is a suite of software for both Macs and PCs, and includes many kinds of software:
- SSH and FTP clients
- Anti-virus software
- Email clients (Outlook Express)
- Modem Dial-up software
- and much more!
This software is free to download for any University staff or student. To go to the download page, click here
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| Protect Yourself And Your Computer! |
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The Internet is no longer a safe place...
As the Internet has increased in popularity, its danger to users has increased dramatically. Despite the best efforts of Internet Security experts, the average user faces many threats including:
- Viruses - These are little pieces of code that embed themselves into larger programs, and are designed to multiply as much as possible...just like real viruses!
- Worms - These are self-sufficient programs whose only purpose is to break into computers, and from there, break into other computers. The results can be devastating.
- Hackers - Contrary to popular belief, hackers don't like to break into your computer because they want to look at your files. Instead hackers break into people's computers for the following reasons:
- They want credit card numbers, or other personal information they can use to steal your idenity.
- They want to use your computer as a starting point to hack other people's computers. If they are caught, it is you who gets into trouble.
- They want to use your computer to store their files (often pornography and illegal music files).
- They want to use your computer's processing power to crack passwords belonging to other people
- They want to use your computer to send junk email to others.
- Some hackers simply enjoy causing destruction and will gladly wipe out all your data just for fun.
- Privacy Invasion - This is a surprisingly common problem. Many commercial websites put small files called "cookies" onto your computer that track what sites you visit and what you links you click on. This is not entirely harmful, but does violate your privacy
So how can you protect yourself?
Fortunately, there are a few simple methods you can do to protect yourself from 95% of the problems out there:
- To protect yourself from viruses, install and run some kind of Anti-Virus software. The UW provides free Anti-Virus software as part of the UWICK kit (see above). To ensure that your Anti-Virus software is up to date, make sure to run its update feature at least once a month, or two months.
- Also, do not open files you do not trust, especially email attachments!
- To protect against worms and hackers, keep the software on your computer (whether its Windows or Macintosh) up to date. Each one has an automatic update feature that you should run weekly:
- In Windows (any version), open Internet Explorer, and click on "tools" then "windows update". Allow it to scan your computer, and choose to install all the critical updates.
- On Mac OS X, click on System Preferences, then Software Update, and then click on the "Check Now" button.
- On Mac OS 9, click on the Apple icon, then go to Control Panel, then Software Update.
- On that note, each of the Operating Systems listed above can also be set to automatically download and install new updates on a set schedule. If you have a DSL or cable modem connection, you can tell it to download and install updates every night while you sleep. This will go a long way to keep out hackers and worms.
- To protect your privacy, be very careful who you give your personal information to, especially credit card information. To block web sites from downloading cookies, you can configure your browser to block all cookies that don't come from the original site. This allows good cookies to get through (such as login cookies), but blocks all the cookies that track your movements for marketing purposes.
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