ASLO Aquatic Sciences meeting – Honolulu, HI


Last week I gave a talk on re-assembling de novo transcriptomes for the MMETSP at the Association for the Sciences of Limnology & Oceanography (ASLO) Aquatic Sciences meeting in Honolulu, HI held at the Hawaii Convention Center from February 27 to March 3, 2017.

Here are links to the latest version of files:

Re-assembly .fasta files for individual MMETSP samples

Repository with pipeline code


Annotation, expression quantification, and peptide translations are also available. About 100 annotations are still incomplete because the dammit pipeline did not finish properly on our HPC, so I’m in the process of re-doing annotations for these.

It was a good experience presenting to a diverse audience of oceanographers, tool users and developers in the session on Advances in Aquatic Meta-Omics: Creating Tools for More Accurate Characterization of Microbial Communities, organized by Brooke Nunn and Emma Timmins-Shiffman. Some good questions and issues came up about the extra content in our re-assemblies compared to NCGR, contamination, and the need to combine multiple samples from the same strain into one assembly.

Special thank you to Harriet Alexander, a postdoc in our lab who was attending the meeting and provided positive feedback and encouragement before my presentation; my advisor, C. Titus Brown for supporting the trip to the meeting; to the DIB lab for helpful feedback prior to the meeting; and, of course, thank you to the Moore Foundation for supporting this work!

Relevant to pushing limits of institutional high performance computing clusters (HPC) with this MMETSP data set (1 TB raw data), while I was away, Amanda Charbonneau wrote this wonderful poem:

ASLO_HIconventionctr.png  LisaCohen_ASLOtalk.png

Overall, I enjoyed the ASLO meeting (click here for #ASLOmtg tweets). I thought that it was well-organized and welcoming to a diversity of participants. In addition to the full schedule of scientific talks, there were many inspiring messages delivered to the aquatic sciences community related to science communication, teamwork, environmental resource sustainability, and gender issues. In a time of political uncertainty regarding environmental protection and the sustainability of public funding for scientific research, it was refreshing to hear senior scientists in leadership positions speak about these topics in a way that left me optimistic for the future.

I was filled with joy during the opening plenary to hear Kalani Quiocho speak about traditional natural resources management practices in Hawai’i and other Pacific islands. He patiently explained to the audience the etymology of several Hawai’ian words, including Ahupua’a (watershed areas), which literally means “cairn” + “pig” because offerings were traditionally made in payment to the chiefs, who were once the watershed resource managers. After the meeting was over and I drove around the island, I noticed road signs denoting different Ahupua’a areas all over the island. This partitioning of land and water resources, local ownership and management by villages and chiefs is common to many Pacific islands. From my time as a Peace Corps Volunteer in Yap (which Kalani showed a picture of in his presentation!), I learned that island cultures and economies are deeply dependent and tied to their land and water resources. With increasing globalization and changing climate, islands are some of the most vulnerable and special environments in the world, capable of serving as miner’s canaries for civilization.

The science presented at this meeting is all contributing towards a better understanding and conservation of all aquatic environments. The technology and -omics tools being developed to analyze a growing volume of data are essential to be able to interpret signals of ecological and biogeochemical significance in our changing environments. I learned about many interesting papers, got some new ideas ideas, and met new people. I do agree that one of the main benefits of attending conferences is the energy derived from networking with people and exchanging ideas.

What a beautiful location to have a meeting.


I also saw and learned the name of the state fish! Humuhumunukunukuāpua‘a, the Hawaaiin Triggerfish.




About Lisa Johnson

PhD candidate at UC Davis in Molecular, Cellular, and Integrative Physiology
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