The SEA-PHAGES Program
SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester, discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses, but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses.
The program aims to increase undergraduate interest and retention in the biological sciences through immediate immersion in authentic, valuable, yet accessible research. By finding and naming their own bacteriophages, students develop a sense of project ownership and have a ready-made personal research project at a fraction of the cost of traditional apprentice-based research programs. Some of the positive effects of the SEA-PHAGES program have been reported here.
SEA-PHAGES is jointly administered by Graham Hatfull's group at the University of Pittsburgh and the Howard Hughes Medical Institute's Science Education division.
The Charlotte Observer | April 16, 2016
Sydney Dishman’s new pet isn’t cute and certainly isn’t something you’d want to cuddle with. But she feels good just thinking about it. Her “pet” is named Rex16, after the Queens University of Charlotte mascot and her year of graduation. Rex16 is a bacteriophage species she discovered while completing her honors research thesis, investigating bacteriophages in local soil samples....read more
Related institution: Queens University of Charlotte
Loquitor—Cabrini College Student Media | March 5, 2011
Surrounded by only her thoughts and glass beekers, one Cabrini student spends much of her time diligently working in the Iadarola Science Center. Katie Mageeney, senior biology major and math and chemistry minor, is anything but an average student. “Katie is definitely dedicated to her lab work,”...read more
Ideation | Sept. 6, 2013
It was the summer that the freshmen ruled the sequencer. Technically, the six William & Mary students who logged heavy lab time with a state-of-the-art Ion Torrent gene sequencer had finished their freshman year and therefore did their summer work as rising sophomores....read more
Related institution: College of William & Mary
Corpus Christi Caller Times | March 29, 2016
Before John Ramirez, 29, decided to go back to school, he worked at Northwest Hospital in Calallen. There, he saw how tuberculosis affected people. "It's almost intensified when you see it," Ramirez said....read more
Related institution: Del Mar College
Gonzaga—The Magazine of Gonzaga University | Aug. 15, 2016
They may have goofy names, but these students’ microscopic pets are serious science. A junior in college, Vina Tran already has a bona fide scientific discovery to her name. Go ahead and look her up on the Actino-bacteriophage Database, a compendium of biological findings maintained by the University of Pittsburgh....read more
Related institution: Gonzaga University
The Brown Daily Herald | Feb. 10, 2012
Sixteen first-years watched with excitement as their screens loaded the sequence of 59,625 nucleic acids that comprise the DNA of “Job42,” the virus a student in their class had discovered, isolated and named during the fall semester. “Each of them codes for something,” said Jordan Rego...read more
Related institution: Brown University
Fusion | May 12, 2015
The scientific journal eLife published a paper on viruses last month—specifically, the genetics of bacteriophages: viruses that infect, and replicate within, bacteria. By sequencing the genomes of individual bacteriophages, or phages, the authors were able to glean information about the genetic makeup of the viruses more broadly.... read more
The College of Idaho—Student News | Aug. 4, 2015
Jetblade. The name might sound like the newest Marvel superhero to hit the big screen, but it’s actually the newest bacterial virus analyzed by College of Idaho students....read more
Related institution: College of Idaho
Science Daily | May 11, 2015
We know that bacteriophages are viruses that infect and replicate within bacteria. We know that they are the most abundant organisms on Earth. But we don't know much about their genetic architecture....read more
Related institution: University of Pittsburgh
Phys.org | June 8, 2016
After sifting through soil samples collected from across Massachusetts, then drilling down to analyze the DNA of viruses they found, a team of undergraduates at Worcester Polytechnic Institute (WPI) hit pay dirt—three potentially novel viruses.... read more
Related institution: Worcester Polytechnic Institute
CU Boulder Today | May 1, 2015
A new study appearing this week in the scientific journal eLIFE about the rapid evolution of small viruses that infect bacteria includes 59 University of Colorado Boulder co-authors, all of whom conducted research for the paper as freshmen....read more
Related institution: University of Colorado at Boulder
Houston Chronicle | Oct. 15, 2016
Brian Blake Maxfeldt likes science just fine, but he didn't go to college expecting to make a discovery his first year. Nevertheless, Maxfeldt, who goes by Blake and graduated from Morton Ranch High School in Katy, discovered a virus that nobody had ever seen before.read more
Related institution: LeTourneau University
wuwf 88.1 | May 12, 2015
The University of West Florida has been chosen to pioneer a unique collaboration between its chemistry and biology departments. Let’s start off with an important definition....read more
Related institution: University of West Florida
Western Carolina News | Sept. 30, 2015
Western Carolina University student Sean Kent didn’t pick the course, but when he saw he was registered for it, the name “Phage Hunters” immediately got his attention. Brooke Burns also found she was placed in the course. After hearing so many other freshmen at orientation say they were excited about WCU’s newest biology/chemistry course, she, too, decided to keep it. Now she says it’s by far her favorite....read more
Related institution: Western Carolina University
innovateKY/YouTube | April 24, 2012
Charles Coomer, a junior in the Honors College at WKU and the son of Evell and Don Coomer, has been involved in microbiological research for two years. In the lab of Dr. Rodney King, associate professor of biology, Coomer is characterizing viruses that infect bacterial cells...read more
Related institution: Western Kentucky University
Written on Nov. 29, 2016 .
Written byon Nov. 16, 2016 .
Thanks to Jeffrey Lawrence, significant changes have been made to the DNA Master code which now allow it to access the newly-secure servers of NCBI. To obtain these changes, you need to update the program. Without updating, important features of DNA Master will not work, including auto-annotation and BLASTing.
To update, open DNA Master then go to Help and click on Update DNA Master. (You will need an internet connection for this to be successful.) You will see a message along the lines of "Update successful upon restarting DNA Master."
After restarting, the following window will appear.
This confirms that DNA Master has been updated to include secure connections. There is also a new Secure Connections panel in the DNA Master Preferences. See below for the suggested values. (These should be the defaults.)
To test that your DNA Master is properly connecting to the new secure NCBI servers, you can try auto-annotating an imported fasta file, then BLASTing one feature from that auto-annotation. If both work, your DNA Master is ready to roll for another year of annotation!
The updated DNA Master is version 5.23.0, build 2487, 15 Nov 2016.
Written byon Nov. 7, 2016 .
NCBI is upgrading its security protocols for programs that contact its servers. DNA Master uses the NCBI servers for both BLAST data and for auto-annotations. At the current time, we have been unable to upgrade DNA Master to use the new protocols, which means auto-annotations and BLASTing through DNA Master will fail.
We are working on it. Thank you for your patience.