2024 Phage Genomics Workshop

Dec 13 to Dec 17, 2024

Workshop

Topic: Annotation & Bioinformatics (in silico)

A week-long workshop where new SEA-PHAGES faculty members learn the basics of the second semester of the course. Topics include auto-annotating a genome, adding or deleting genes, calling tRNAs, refining start-site calls, merging annotations, determining functions, and comparative genomics. The two major programs used are DNA Master and Phamerator, both of which participants should be well-acquainted with by the end of the workshop.

2024 Phage Discovery Workshop 17B

Jul 13 to Jul 19, 2024

Workshop

Topic: Microbiology (in situ)

The goal of the workshop is to familiarize the new cohort 16 schools as well as several of the faculty that have been added previously, but have not had formal training. Participants with get to know the concepts and associated techniques of bacteriophage isolation and characterization. Another important component is to share experiences in pedagogy and reagent/supply acquisition and preparation that will help with the implementation of the course at each institution. One of the benefits of being part of the SEA-PHAGES community is the support available from each cohort and the large number of other SEA-PHAGES institutions. This benefit also extends to the students with the knowledge that they are part of a larger scientific community and that their research efforts are valued.

2024 Phage Discovery Workshop 17A

Jun 22 to Jun 28, 2024

Workshop

Topic: Microbiology (in situ)

The goal of the workshop is to familiarize the new cohort 16 schools as well as several of the faculty that have been added previously, but have not had formal training. Participants with get to know the concepts and associated techniques of bacteriophage isolation and characterization. Another important component is to share experiences in pedagogy and reagent/supply acquisition and preparation that will help with the implementation of the course at each institution. One of the benefits of being part of the SEA-PHAGES community is the support available from each cohort and the large number of other SEA-PHAGES institutions. This benefit also extends to the students with the knowledge that they are part of a larger scientific community and that their research efforts are valued.

2023 Phage Genomics Workshop

Dec 4 to Dec 8, 2023

Workshop

Topic: Annotation & Bioinformatics (in silico)

A week-long workshop where new SEA-PHAGES faculty members learn the basics of the second semester of the course. Topics include auto-annotating a genome, adding or deleting genes, calling tRNAs, refining start-site calls, merging annotations, determining functions, and comparative genomics. The two major programs used are DNA Master and Phamerator, both of which participants should be well-acquainted with by the end of the workshop. Steve's Observable Notebook https://observablehq.com/@cresawn-labs/sea-bioinformatics-workshop-2023 CNN International "Viruses Fighting Bacteria" https://www.cnn.com/videos/health/2023/12/05/phages-antibiotic-resistance-research-vital-signs-intl-spc.cnn

2023 Phage Discovery Workshop 16B

Jul 8 to Jul 14, 2023

Workshop

Topic: Microbiology (in situ)

The goal of the workshop is to familiarize the new cohort 16 schools as well as several of the faculty that have been added previously, but have not had formal training. Participants with get to know the concepts and associated techniques of bacteriophage isolation and characterization. Another important component is to share experiences in pedagogy and reagent/supply acquisition and preparation that will help with the implementation of the course at each institution. One of the benefits of being part of the SEA-PHAGES community is the support available from each cohort and the large number of other SEA-PHAGES institutions. This benefit also extends to the students with the knowledge that they are part of a larger scientific community and that their research efforts are valued.

2023 Phage Discovery Workshop 16A

Jun 24 to Jun 30, 2023

Workshop

Topic: Microbiology (in situ)

The goal of the workshop is to familiarize the new cohort 16 schools as well as several of the faculty that have been added previously, but have not had formal training. Participants with get to know the concepts and associated techniques of bacteriophage isolation and characterization. Another important component is to share experiences in pedagogy and reagent/supply acquisition and preparation that will help with the implementation of the course at each institution. One of the benefits of being part of the SEA-PHAGES community is the support available from each cohort and the large number of other SEA-PHAGES institutions. This benefit also extends to the students with the knowledge that they are part of a larger scientific community and that their research efforts are valued.

2022 Phage Genomics Workshop

Dec 5 to Dec 9, 2022

Workshop

Topic: Annotation & Bioinformatics (in silico)

A week-long workshop where new SEA-PHAGES faculty members learn the basics of the second semester of the course. Topics include auto-annotating a genome, adding or deleting genes, calling tRNAs, refining start-site calls, merging annotations, determining functions, and comparative genomics. The two major programs used are DNA Master and Phamerator, both of which participants should be well-acquainted with by the end of the workshop. SEA-PHAGES Bioinformatics Guide

Phage Discovery Workshop 15B

Jul 9 to Jul 15, 2022

Workshop

Topic: Microbiology (in situ)

The goal of the workshop is to familiarize the new cohort 15 schools as well as several of the faculty that have been added previously, but have not had formal training. Participants with get to know the concepts and associated techniques of bacteriophage isolation and characterization. Another important component is to share experiences in pedagogy and reagent/supply acquisition and preparation that will help with the implementation of the course at each institution. One of the benefits of being part of the SEA-PHAGES community is the support available from each cohort and the large number of other SEA-PHAGES institutions. This benefit also extends to the students with the knowledge that they are part of a larger scientific community and that their research efforts are valued.

2022 Phage Discovery Workshop 15A

Jun 25 to Jul 1, 2022

Workshop

Topic: Microbiology (in situ)

The goal of the workshop is to familiarize the new cohort 15 schools as well as several of the faculty that have been added previously, but have not had formal training. Participants with get to know the concepts and associated techniques of bacteriophage isolation and characterization. Another important component is to share experiences in pedagogy and reagent/supply acquisition and preparation that will help with the implementation of the course at each institution. One of the benefits of being part of the SEA-PHAGES community is the support available from each cohort and the large number of other SEA-PHAGES institutions. This benefit also extends to the students with the knowledge that they are part of a larger scientific community and that their research efforts are valued.

2022 SEA Faculty Meeting

Jun 3 to Jun 3, 2022

Workshop

A virtual meeting to which all SEA faculty are invited. We'll share program updates, have faculty presentations, facilitate conversations, and work in groups on items relevant to the SEA's programs.

Cohort 14 Phage Genomics Workshop (Dec 2021)

Dec 6 to Dec 17, 2021

Workshop

Topic: Annotation & Bioinformatics (in silico)

November 12, 2021 Virtual Faculty Meeting: Bioinformatics Update

Nov 12 to Nov 12, 2021

Workshop

Topic: Annotation & Bioinformatics (in silico)

More information about this meeting can be found on the Monthly Virtual Faculty Meetings forum page.

September 10, 2021 Virtual Faculty Meeting: Host Range Journal Club

Sep 10 to Sep 10, 2021

Workshop

Topic: Microbiology (in situ)

More information about this meeting can be found on the Monthly Virtual Faculty Meetings forum page.

2021 GENES Faculty Workshop

Jun 15 to Jun 16, 2021

Workshop

2021 SEA Faculty Meeting

Jun 7 to Jun 9, 2021

Workshop

Gathering of SEA Faculty to Share and Work on Program Related Activities.

Cohort 13 Phage Genomics Workshop (Dec 2020)

Dec 7 to Dec 18, 2020

Workshop

Topic: Annotation & Bioinformatics (in silico)

Please use the following information to access the workshop from a computer https://hhmi.zoom.us/j/97323945108 Meeting ID: 973 2394 5108 Password: 1111

Cohort 13 Phage Genomics Workshop (June 2020)

Jun 15 to Jun 26, 2020

Workshop

Topic: Annotation & Bioinformatics (in silico)

This meeting will be hosted on Zoom: Link: https://pitt.zoom.us/j/97135496272 Meeting #: 97135496272

2019 Phage Genomics Workshop

Dec 9 to Dec 13, 2019

Workshop

Topic: Annotation & Bioinformatics (in silico)

A week-long workshop where new SEA-PHAGES faculty members learn the basics of the second semester of the course. Topics include auto-annotating a genome, adding or deleting genes, calling tRNAs, refining start-site calls, merging annotations, determining functions, and comparative genomics. The two major programs used are DNA Master and Phamerator, both of which participants should be well-acquainted with by the end of the workshop. Update: BodEinwohner17 has been submitted to GenBank, accession # MN945900. The DNA Master file is available on its phage page. Check out how you did with your own version of the annotation by using the "Review to Improve" protocol in the Bioinformatics Guide. SEA-PHAGES Bioinformatics Guide BodEinwohner17 Gene Sign-up Sheet

Phage Discovery Workshop 12B

Jul 7 to Jul 13, 2019

Workshop

Topic: Microbiology (in situ)

The goal of the workshop is to familiarize the new cohort 12 schools with the concepts and associated techniques of bacteriophage isolation and characterization. Another important component is to share experiences in pedagogy and reagent/supply acquisition and preparation that will help with the implementation of the course at each institution. One of the benefits of being part of the SEA-PHAGES community is the support available from each cohort and the large number of other SEA-PHAGES institutions. This benefit also extends to the students with the knowledge that they are part of a larger scientific community and that their research efforts are valued.

Phage Discovery Workshop 12A

Jun 22 to Jun 28, 2019

Workshop

Topic: Microbiology (in situ)

The goal of the workshop is to familiarize the new cohort 12 schools with the concepts and associated techniques of bacteriophage isolation and characterization. Another important component is to share experiences in pedagogy and reagent/supply acquisition and preparation that will help with the implementation of the course at each institution. One of the benefits of being part of the SEA-PHAGES community is the support available from each cohort and the large number of other SEA-PHAGES institutions. This benefit also extends to the students with the knowledge that they are part of a larger scientific community and that their research efforts are valued.

2019 SEA Microbacterium Genomics Workshop

Jun 9 to Jun 11, 2019

Workshop

Topic: Advanced Bioinformatics

This meeting will focus on comparative genomics of the first 117 sequenced Microbacterium phages. Participants will work together to learn advanced bioinformatics tools and create products that can be used in a descriptive paper about these phages. What to bring: You must bring a laptop with a working copy of DNA Master. We strongly recommend that this computer also have: -a working copy of the 2017 SEA VM -some kind of graphics software like Illustrator, Inkscape, or Canvas -Excel -SplitsTree (splitstree.org) which requires Java -PhamNexus https://github.com/chg60/phamnexus/wiki (at the moment, PhamNexus only runs on Linux. PhamNexus generates the files that SplitsTree uses as input, so if you do not want to make SplitsTree files, you do not have to run this program). IF you no longer have the SEA VM on your computer, we have a new version formatted for Virtual Box with PhamNexus and the Phamerator QC program pre-installed: https://www.dropbox.com/s/nreonw7wuov10tc/Updated_2017_SEAVM.zip?dl=0 Before the workshop: Review similar papers on phage genomics (Arthrobacter paper, Gordonia paper) https://www.ncbi.nlm.nih.gov/pubmed/29437090 https://www.ncbi.nlm.nih.gov/pubmed/28811342 Install Phamnexus and SplitsTree Google Doc with Post-It Details https://docs.google.com/document/d/19o2TmW8xATtfacrgMJcTS_cR_LVWIdtDsSRF52mxxQk/edit?usp=sharing Link to submit products: https://www.dropbox.com/request/wpzI1Vx7yqZjKsc4bppQ

2019 SEA GENES Faculty Meeting

Jun 9 to Jun 11, 2019

Workshop

This meeting is a focused workshop for SEA Faculty who will implement the SEA-GENES project as part of Cohort 1 in the 2019-2020 academic year.

2018 Bioinformatics Workshop

Dec 10 to Dec 14, 2018

Workshop

Topic: Annotation & Bioinformatics (in silico)

A week-long workshop where new SEA-PHAGES faculty members learn the basics of the second semester of the course. Topics include auto-annotating a genome, adding or deleting genes, calling tRNAs, refining start-site calls, merging annotations, determining functions, and comparative genomics. The two major programs used are DNA Master and Phamerator, both of which participants should be well-acquainted with by the end of the workshop. SEA-PHAGES Bioinformatics Guide Agenda with links to guide: https://docs.google.com/document/d/1sLXur88RU71YGUXxw3uU7B3UThSBjmGs75vcwATWgJo/

Phage Discovery Workshop 11B

Jul 7 to Jul 13, 2018

Workshop

Topic: Microbiology (in situ)

The goal of the workshop is to familiarize the new cohort 11 schools with the concepts and associated techniques of bacteriophage isolation and characterization. Another important component is to share experiences in pedagogy and reagent/supply acquisition and preparation that will help with the implementation of the course at each institution. One of the benefits of being part of the SEA-PHAGES community is the support available from each cohort and the large number of other SEA-PHAGES institutions. This benefit also extends to the students with the knowledge that they are part of a larger scientific community and that their research efforts are valued.

Phage Discovery Workshop 11A

Jun 23 to Jun 29, 2018

Workshop

Topic: Microbiology (in situ)

The goal of the workshop is to familiarize the new cohort 11 schools with the concepts and associated techniques of bacteriophage isolation and characterization. Another important component is to share experiences in pedagogy and reagent/supply acquisition and preparation that will help with the implementation of the course at each institution. One of the benefits of being part of the SEA-PHAGES community is the support available from each cohort and the large number of other SEA-PHAGES institutions. This benefit also extends to the students with the knowledge that they are part of a larger scientific community and that their research efforts are valued.

SEA-PHAGES Faculty Meeting 2018

Jun 10 to Jun 12, 2018

Workshop

SEA-PHAGES Faculty Meeting 2018 Survey Link

2017 Bioinformatics Workshop

Dec 8 to Dec 12, 2017

Workshop

Topic: Annotation & Bioinformatics (in silico)

Participants will be able to annotate a phage genome, RagingRooster. SEA-PHAGES Bioinformatics Guide: https://seaphagesbioinformatics.helpdocsonline.com/ Spreadsheet for draft function annotation: Here

Phage Discovery Workshop 10B

Jul 8 to Jul 14, 2017

Workshop

Topic: Microbiology (in situ)

The goal of the workshop is to familiarize the new cohort 10 schools with the concepts and associated techniques of bacteriophage isolation and characterization. Another important component is to share experiences in pedagogy and reagent/supply acquisition and preparation that will help with the implementation of the course at each institution. One of the benefits of being part of the SEA-PHAGES community is the support available from each cohort and the large number of other SEA-PHAGES institutions. This benefit also extends to the students with the knowledge that they are part of a larger scientific community and that their research efforts are valued.

Phage Discovery Workshop 10A

Jun 24 to Jun 30, 2017

Workshop

Topic: Microbiology (in situ)

The goal of the workshop is to familiarize the new cohort 10 schools with the concepts and associated techniques of bacteriophage isolation and characterization. Another important component is to share experiences in pedagogy and reagent/supply acquisition and preparation that will help with the implementation of the course at each institution. One of the benefits of being part of the SEA-PHAGES community is the support available from each cohort and the large number of other SEA-PHAGES institutions. This benefit also extends to the students with the knowledge that they are part of a larger scientific community and that their research efforts are valued.

2017 Genome Announcement Workshop

Jun 11 to Jun 13, 2017

Workshop

Topic: Advanced Bioinformatics

In lieu of the standard biennial Advanced Bioinformatics Workshop, this year we will host a Genome Announcement Workshop following the 9th Annual SEA-PHAGES Symposium in June. Instead of a single paper describing in-depth analyses of a group of phages, this year’s workshop will focus on helping participants produce their own high-quality genome announcements. The facilitators will demonstrate the use of bioinformatic tools to tease out interesting genomic features, and will provide guidance about the particulars of writing this very specific type of paper. Participants will then work in small teams to write a genome announcement for a related group of phages, including their own. ICMJE Guidelines Genome Announcements Instructions to Authors

2016 SEA-PHAGES Bioinformatics Workshop

Dec 5 to Dec 9, 2016

Workshop

Topic: Annotation & Bioinformatics (in silico)

An intensive week-long workshop where new SEA-PHAGES faculty members learn the basics of the second semester of the course. Topics include auto-annotating a genome, adding or deleting genes, calling tRNAs, refining start-site calls, merging annotations, determining functions, and comparative genomics. The two major programs used are DNA Master and Phamerator, both of which participants should be well-acquainted with by the end of the workshop. CrystalP was successfully submitted to GenBank on Friday, December 9, 2016 with a release date of January 15, 2017. Accession # is KY319168.

Phage Discovery Workshop 9B

Jul 10 to Jul 15, 2016

Workshop

Topic: Microbiology (in situ)

The goal of the workshop is to familiarize the new cohort 9 schools with the concepts and associated techniques of bacteriophage isolation and characterization. Another important component is to share experiences in pedagogy and reagent/supply acquisition and preparation that will help with the implementation of the course at each institution. One of the benefits of being part of the SEA-PHAGES community is the support available from each cohort and the large number of other SEA-PHAGES institutions. This benefit also extends to the students with the knowledge that they are part of a larger scientific community and that their research efforts are valued.

Phage Discovery Workshop 9A

Jun 26 to Jul 1, 2016

Workshop

Topic: Microbiology (in situ)

The goal of the workshop is to familiarize the new cohort 9 schools with the concepts and associated techniques of bacteriophage isolation and characterization. Another important component is to share experiences in pedagogy and reagent/supply acquisition and preparation that will help with the implementation of the course at each institution. One of the benefits of being part of the SEA-PHAGES community is the support available from each cohort and the large number of other SEA-PHAGES institutions. This benefit also extends to the students with the knowledge that they are part of a larger scientific community and that their research efforts are valued.

2016 SEA-PHAGES Faculty Workshop

Jun 12 to Jun 14, 2016

Workshop

A gathering for faculty members currently active in the SEA-PHAGES program. One goal is to inform faculty of the improvements and developments in the program. Another goal is to have worthwhile working sessions for the faculty to create meaningful products that can be used by others in the program.

2015 SEA-PHAGES Bioinformatics Workshop

Dec 7 to Dec 11, 2015

Workshop

Topic: Annotation & Bioinformatics (in silico)

An intensive week-long workshop where new SEA-PHAGES faculty members learn the basics of the second semester of the course. Topics include auto-annotating a genome, adding or deleting genes, calling tRNAs, refining start-site calls, merging annotations, determining functions, and comparative genomics. The two major programs used are DNA Master and Phamerator, both of which participants should be well-acquainted with by the end of the workshop. View live stream here, when available, or archived videos of presentations: http://mediasiteex.hhmi.org/Mediasite/Catalog/Full/672215ce45df45caa93499b86d49c64821

In Situ Workshop 8B

Jul 12 to Jul 17, 2015

Workshop

Topic: Microbiology (in situ)

The goal of the workshop is to familiarize the new cohort 8 schools with the concepts and associated techniques of bacteriophage isolation and characterization. Another important component is to share experiences in pedagogy and reagent/supply acquisition and preparation that will help with the implementation of the course at each institution. One of the benefits of being part of the SEA-PHAGES community is the support available from each cohort and the large number of other SEA-PHAGES institutions. This benefit also extends to the students with the knowledge that they are part of a larger scientific community and that their research efforts are valued.

In Situ Workshop 8A

Jun 21 to Jun 26, 2015

Workshop

Topic: Microbiology (in situ)

The goal of the workshop is to familiarize the new cohort 8 schools with the concepts and associated techniques of bacteriophage isolation and characterization. Another important component is to share experiences in pedagogy and reagent/supply acquisition and preparation that will help with the implementation of the course at each institution. One of the benefits of being part of the SEA-PHAGES community is the support available from each cohort and the large number of other SEA-PHAGES institutions. This benefit also extends to the students with the knowledge that they are part of a larger scientific community and that their research efforts are valued.

2015 Advanced Bioinformatics Workshop

Jun 15 to Jun 17, 2015

Workshop

Topic: Advanced Bioinformatics

At this year's Advanced Bioinformatics Workshop, approximately 30 SEA-PHAGES faculty members will investigate the genomes of Cluster N phages. The genome and gene sequences are available at PhagesDB and Phamerator, with some still under final review, though all will be finalized by the workshop. Students and faculty at Lehigh, Southern Connecticut State and Pitt are doing some wet bench experiments that include electron microscopy, lysogeny and immunity testing along with preliminary bioinformatic analyses. A draft agenda is now available.

Inaugural GIFT Workshop

Dec 8 to Dec 10, 2014

Workshop

Topic: Genome Inspection and Finishing

Attendees of this workshop will learn to assemble, quality-control, and finish genomes from a variety of sequencing technologies. The attendees will then form the first SEA-PHAGES Genome Inspection and Finishing Team (GIFT), responsible for assembling and finishing genomes sequenced for participating SEA-PHAGES member institutions.

2014 SEA-PHAGES In Silico Workshop

Dec 8 to Dec 12, 2014

Workshop

Topic: Annotation & Bioinformatics (in silico)

An intensive week-long workshop where new SEA-PHAGES faculty members learn the basics of the second semester of the course. Topics include auto-annotating a genome, adding or deleting genes, calling tRNAs, refining start-site calls, merging annotations, determining functions, and comparative genomics. The two major programs used are DNA Master and Phamerator, both of which participants should be well-acquainted with by the end of the workshop.