Author Archives: Robert

Replace the printer cartridge

At some point, the lab printer will run out of toner and the cartridge has to be replaced. New printer cartrigdes can be found in the mail room in 411. If you don’t have a key for 411, ask someone who has a key to help you. If there is no printer cartridge for the model you need, ask Brenda in the office to order a new one (tell her the Q-number from below). Ordering a new cartrigde takes 2-3 days. (In case Brenda asks, tell her that Amy will take care of the payment.)
Current lab printer: HP 2420
Printer cartridge: 11A (Q6511A)
Some last notes for cartridge recycling. The old cartridge should be packed into the box of the new cartridge. Put the provided return sticker on top when you are done (or go to to print a free return shipping label). The easiest way to get the box shipped back to HP is to leave it in the outgoing mailbox in 411 (in the room with the table, after the second door). That’s all.

Achievement Rewards for College Scientists (ARCS)

The San Diego Chapter of the ARCS (Achievement Rewards for College Scientists) Foundation is one of 17 chapters that are dedicated to helping the best and brightest United States students by providing scholar awards in the natural sciences, medicine, and engineering. For academic year 2009-2010, ARCS Foundation chapters contributed $4,000,961 to 519 students at 52 colleges and universities.

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IRA Funds for student travel to professional meetings

The College of Sciences receives Instructionally Related Activities (IRA) funds to help support student travel to professional meetings to present the results of their research. In order, to apply for IRA funds, the student must be enrolled in a College of Sciences undergraduate or graduate program. The following are guidelines for requesting travel funds:

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How to run BLAST on a compressed FASTA file

FASTA files with sequences from next-generation sequencing projects can be large and are usually stored as compressed files using compression algorithms such as GZIP or ZIP. If you do not want to extract all the data or create another copy of the file when performing a BLAST search, you can combine the file extraction and the BLAST search using a pipe in Unix-based operating systems and tell the BLAST program to use the standard input. Here is one example on how to do that (assuming you have a GZIP compressed FASTA file): Continue reading

How to remove human DNA sequence contamination from metagenomes

The immense amount of metagenomic data produced today requires an automated approach for data processing and analysis. Before any downstream analysis will be performed, the datasets should be preprocessed to ensure the quality of the data and prevent erroneous conclusions. One step of your data preprocessing (usually the last) should be to check for sequence contamination (DNA from sources other than the sample). This post will show you how to identify and remove human sequence contamination from metagenomes, but can also be applied to any other type of sequence dataset or contamination.

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Transition in Vibrio spp. correlates with human activity in the Northern Line Islands

Robert Schmieder, Tracy McDole, Elizabeth Dinsdale, Matthew Haynes, Forest Rohwer, Robert Edwards

Presented at: International Coral Reef Symposium (ICRS) 2008
Download PDF file (3.5 MB)


ADAPTdb/ADAPT – A Framework for the Analysis of ARISA Data Sets

Robert Schmieder, Matthew Haynes, Elizabeth Dinsdale, Forest Rohwer, and Robert Edwards

Presented at: Metagenomics 2008
Download PDF file (1.2 MB)