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    <title>Alexander Lab @ WHOI on Alexander Lab @ WHOI</title>
    <link>https://alexanderlabwhoi.github.io/</link>
    <description>Recent content in Alexander Lab @ WHOI on Alexander Lab @ WHOI</description>
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    <copyright>&amp;copy; 2019</copyright>
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    <item>
      <title>A case for absolute gene expression estimates in microbiome studies using metatranscriptomics</title>
      <link>https://alexanderlabwhoi.github.io/publication/perneel-2025-case/</link>
      <pubDate>Wed, 01 Jan 2025 00:00:00 -0500</pubDate>
      
      <guid>https://alexanderlabwhoi.github.io/publication/perneel-2025-case/</guid>
      <description></description>
    </item>
    
    <item>
      <title>Exploring the Phaeosphere: Characterizing the microbiomes of Phaeocystis antarctica colonies from the coastal Southern Ocean and laboratory culture</title>
      <link>https://alexanderlabwhoi.github.io/publication/mars-2024-exploring/</link>
      <pubDate>Wed, 01 Jan 2025 00:00:00 -0500</pubDate>
      
      <guid>https://alexanderlabwhoi.github.io/publication/mars-2024-exploring/</guid>
      <description></description>
    </item>
    
    <item>
      <title>Intraspecific diversity in thermal performance determines phytoplankton ecological niche</title>
      <link>https://alexanderlabwhoi.github.io/publication/krinos-2025-intraspecific/</link>
      <pubDate>Wed, 01 Jan 2025 00:00:00 -0500</pubDate>
      
      <guid>https://alexanderlabwhoi.github.io/publication/krinos-2025-intraspecific/</guid>
      <description></description>
    </item>
    
    <item>
      <title>Microbial Ecology to Ocean Carbon Cycling: From Genomes to Numerical Models</title>
      <link>https://alexanderlabwhoi.github.io/publication/levine-2025-microbial/</link>
      <pubDate>Wed, 01 Jan 2025 00:00:00 -0500</pubDate>
      
      <guid>https://alexanderlabwhoi.github.io/publication/levine-2025-microbial/</guid>
      <description></description>
    </item>
    
    <item>
      <title>Microeukaryote metabolism across the western North Atlantic Ocean revealed through autonomous underwater profiling</title>
      <link>https://alexanderlabwhoi.github.io/publication/cohen-2024-microeukaryote/</link>
      <pubDate>Mon, 01 Jan 2024 00:00:00 -0500</pubDate>
      
      <guid>https://alexanderlabwhoi.github.io/publication/cohen-2024-microeukaryote/</guid>
      <description></description>
    </item>
    
    <item>
      <title>Missing microbial eukaryotes and misleading meta-omic conclusions</title>
      <link>https://alexanderlabwhoi.github.io/publication/krinos-2024-missing/</link>
      <pubDate>Mon, 01 Jan 2024 00:00:00 -0500</pubDate>
      
      <guid>https://alexanderlabwhoi.github.io/publication/krinos-2024-missing/</guid>
      <description></description>
    </item>
    
    <item>
      <title>Molecular forecasting of toxic bloom events</title>
      <link>https://alexanderlabwhoi.github.io/publication/alexander-2024-molecular/</link>
      <pubDate>Mon, 01 Jan 2024 00:00:00 -0500</pubDate>
      
      <guid>https://alexanderlabwhoi.github.io/publication/alexander-2024-molecular/</guid>
      <description></description>
    </item>
    
    <item>
      <title>The Dawn of the BioGeoSCAPES Program</title>
      <link>https://alexanderlabwhoi.github.io/publication/saito-2024-dawn/</link>
      <pubDate>Mon, 01 Jan 2024 00:00:00 -0500</pubDate>
      
      <guid>https://alexanderlabwhoi.github.io/publication/saito-2024-dawn/</guid>
      <description></description>
    </item>
    
    <item>
      <title>sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets</title>
      <link>https://alexanderlabwhoi.github.io/publication/irber-2024-sourmash/</link>
      <pubDate>Mon, 01 Jan 2024 00:00:00 -0500</pubDate>
      
      <guid>https://alexanderlabwhoi.github.io/publication/irber-2024-sourmash/</guid>
      <description></description>
    </item>
    
    <item>
      <title>Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly</title>
      <link>https://alexanderlabwhoi.github.io/publication/krinos-2023/</link>
      <pubDate>Wed, 01 Mar 2023 00:00:00 -0500</pubDate>
      
      <guid>https://alexanderlabwhoi.github.io/publication/krinos-2023/</guid>
      <description></description>
    </item>
    
    <item>
      <title>Using anvi&#39;o in interactive mode</title>
      <link>https://alexanderlabwhoi.github.io/post/2022-10-24_anvio/</link>
      <pubDate>Mon, 24 Oct 2022 15:25:12 -0400</pubDate>
      
      <guid>https://alexanderlabwhoi.github.io/post/2022-10-24_anvio/</guid>
      <description>

&lt;p&gt;Anvi&amp;rsquo;o is a powerful tool for analyzing and vizualizing &amp;lsquo;omics data, much of which relies on one&amp;rsquo;s ability to visualize those data. On Poseidon, it can sometimes be difficult to work with these kinds of plotting tools, because we&amp;rsquo;re working on the command line. To use anvi&amp;rsquo;o interactively on Poseidon, we need to go through a few extra steps.&lt;/p&gt;

&lt;p&gt;I&amp;rsquo;ll walk you through the whole installation of anvi&amp;rsquo;o here from start to finish! Most of these instructions are also available on anvio.org. The other half of these instructions are mostly in the posts &lt;a href=&#34;https://alexanderlabwhoi.github.io/post/2019-03-08_jpn_slurm/&#34; target=&#34;_blank&#34;&gt;here&lt;/a&gt; (for Mac) and &lt;a href=&#34;https://alexanderlabwhoi.github.io/post/2019-07-24-slurm-win/&#34; target=&#34;_blank&#34;&gt;here&lt;/a&gt; (for Windows) that we&amp;rsquo;ve previously uploaded to the blog!&lt;/p&gt;

&lt;h3 id=&#34;step-one-create-a-fresh-conda-environment-for-anvi-o-and-install-dependencies&#34;&gt;Step One: create a fresh &lt;code&gt;conda&lt;/code&gt; environment for anvi&amp;rsquo;o and install dependencies&lt;/h3&gt;

&lt;p&gt;I like using &lt;code&gt;mamba&lt;/code&gt;. That will make the rest of your installs much faster. So I&amp;rsquo;ve modified anvi&amp;rsquo;o&amp;rsquo;s installation instructions a little bit to fit that principle. After logging into Poseidon&amp;rsquo;s login node (and making sure that you have the most recent and/or your preferred anaconda module loaded), we&amp;rsquo;ll run:&lt;/p&gt;

&lt;pre&gt;&lt;code&gt;conda create -y --name anvio python=3.6 mamba
&lt;/code&gt;&lt;/pre&gt;

&lt;p&gt;We&amp;rsquo;ll wait for that to finish, then execute &lt;code&gt;conda activate anvio&lt;/code&gt; (or whatever you chose to name your environment! Next, we have a whole list of packages we&amp;rsquo;ll want mamba to go ahead and (efficiently) install for us in order for anvi&amp;rsquo;o to work. You should be able to just copy, paste, and execute this entire code block right in your terminal window.&lt;/p&gt;

&lt;pre&gt;&lt;code&gt;mamba install -y -c bioconda &amp;quot;sqlite&amp;gt;=3.31.1&amp;quot;
mamba install -y -c bioconda prodigal
mamba install -y -c bioconda mcl
mamba install -y -c bioconda muscle=3.8.1551
mamba install -y -c bioconda hmmer
mamba install -y -c bioconda diamond
mamba install -y -c bioconda blast
mamba install -y -c bioconda megahit
mamba install -y -c bioconda spades
mamba install -y -c bioconda bowtie2 tbb=2019.8
mamba install -y -c bioconda bwa
mamba install -y -c bioconda samtools=1.9
mamba install -y -c bioconda centrifuge
mamba install -y -c bioconda trimal
mamba install -y -c bioconda iqtree
mamba install -y -c bioconda trnascan-se
mamba install -y -c bioconda r-base
mamba install -y -c bioconda r-stringi
mamba install -y -c bioconda r-tidyverse
mamba install -y -c bioconda r-magrittr
mamba install -y -c bioconda r-optparse
mamba install -y -c bioconda bioconductor-qvalue
mamba install -y -c bioconda fasttree
mamba install -y -c bioconda vmatch
mamba install -y -c bioconda fastani ## anvio says you don&#39;t need this one
&lt;/code&gt;&lt;/pre&gt;

&lt;p&gt;Note: anvi&amp;rsquo;o&amp;rsquo;s website says that you don&amp;rsquo;t need the &lt;code&gt;fastani&lt;/code&gt; package installed for the software to work. The install went fine for me. The whole install process might take quite a while, depending on the speed of the connection. If you elect to use &lt;code&gt;conda&lt;/code&gt; over &lt;code&gt;mamba&lt;/code&gt;, it will take a &lt;em&gt;lot&lt;/em&gt; longer.&lt;/p&gt;

&lt;h3 id=&#34;step-two-actually-install-anvi-o&#34;&gt;Step Two: actually install anvi&amp;rsquo;o&lt;/h3&gt;

&lt;p&gt;You should execute this in a folder where you don&amp;rsquo;t mind software files being downloaded to:&lt;/p&gt;

&lt;pre&gt;&lt;code&gt;curl -L https://github.com/merenlab/anvio/releases/download/v7.1/anvio-7.1.tar.gz \
        --output anvio-7.1.tar.gz
pip install anvio-7.1.tar.gz
&lt;/code&gt;&lt;/pre&gt;

&lt;p&gt;Now, you should be good to go to run anvi&amp;rsquo;o!&lt;/p&gt;

&lt;h3 id=&#34;step-three-get-a-worker-node-spun-up-to-do-your-bidding&#34;&gt;Step Three: get a worker node spun up to do your bidding&lt;/h3&gt;

&lt;p&gt;We&amp;rsquo;ll run an interactive job on Poseidon using &lt;code&gt;srun&lt;/code&gt;. You can modify this command as needed if you want this job to go for longer than two hours&amp;hellip;or if people are hogging all the &lt;code&gt;compute&lt;/code&gt; nodes and you need to hedge your bets with a pre-empt-able &lt;code&gt;scavenger&lt;/code&gt; run, for example.&lt;/p&gt;

&lt;pre&gt;&lt;code&gt;srun -p compute --time=02:00:00 --mem=50gb --pty bash
&lt;/code&gt;&lt;/pre&gt;

&lt;p&gt;Eventually, this should log you into a clean worker node, so your prompt should change from &lt;username&gt;@poseidon-l&lt;1 or 2&gt;.whoi.edu to &lt;username&gt;@pn&amp;lt;# of node you were assigned&amp;gt;. Now, you&amp;rsquo;re ready to not annoy the IT department by executing expensive programs on the common login node! Make sure now to &lt;code&gt;conda activate anvio&lt;/code&gt;.&lt;/p&gt;

&lt;h3 id=&#34;step-four-run-anvi-o-interactive-but-make-sure-to-specify-a-port&#34;&gt;Step Four: run anvi&amp;rsquo;o interactive, but make sure to specify a port&lt;/h3&gt;

&lt;p&gt;In order to run this, I am going to use the example the &lt;a href=&#34;https://merenlab.org/2016/02/27/the-anvio-interactive-interface/&#34; target=&#34;_blank&#34;&gt;Eren lab&lt;/a&gt; provides, since I don&amp;rsquo;t use anvi&amp;rsquo;o much. Note that their link is broken on their tutorial website. I found one that works &lt;a href=&#34;https://github.com/meren/anvio/blob/master/anvio/tests/sandbox/example-newick-tree.txt&#34; target=&#34;_blank&#34;&gt;here&lt;/a&gt;. I just saved the Newick text at that link to a file called &lt;code&gt;meren_tree.txt&lt;/code&gt;, then (inside my interactive session!), I executed:&lt;/p&gt;

&lt;pre&gt;&lt;code&gt;anvi-interactive -t meren_tree.txt -p profile.db --title &#39;Simple tree test&#39; --server-only -P 5785
&lt;/code&gt;&lt;/pre&gt;

&lt;h3 id=&#34;step-five-log-into-your-node-and-forward-that-port-to-your-browser&#34;&gt;Step Five: log into your node and forward that port to your browser&lt;/h3&gt;

&lt;p&gt;All of these steps are straight out of our tutorial on running a Jupyter notebook remotely that I linked above. If you use Windows, be sure to check out that post - I&amp;rsquo;m only using the Mac command here.&lt;/p&gt;

&lt;pre&gt;&lt;code&gt;ssh -t -t &amp;lt;username&amp;gt;@poseidon-l1.whoi.edu -L 5785:localhost:5785 ssh &amp;lt;the name of the &amp;quot;pn&amp;quot; node from above that showed up when you ran srun&amp;gt; -L 5785:localhost:5785
&lt;/code&gt;&lt;/pre&gt;

&lt;p&gt;To summarize, above you need to swap out:
- your own username
- the port number if you changed it
- the name of the worker node you ssh&amp;rsquo;d into&lt;/p&gt;

&lt;p&gt;For example, if my username is &amp;ldquo;akrinos&amp;rdquo;, I used port 5786, and I ssh&amp;rsquo;d into &amp;ldquo;pn075&amp;rdquo;, I would type:&lt;/p&gt;

&lt;pre&gt;&lt;code&gt;ssh -t -t akrinos@poseidon-l1.whoi.edu -L 5786:localhost:5786 ssh pn075 -L 5786:localhost:5786
&lt;/code&gt;&lt;/pre&gt;

&lt;p&gt;Be sure to check out our more detailed post on ssh tunneling if you want shortcuts for doing this!&lt;/p&gt;

&lt;h3 id=&#34;step-six-access-your-interactive-session&#34;&gt;Step Six: access your interactive session&lt;/h3&gt;

&lt;p&gt;Simply type &lt;code&gt;localhost:5786&lt;/code&gt; into your web browser (replacing this second number with your present node), and you should be able to see your anvi&amp;rsquo;o interactive session! Feel free to use any &lt;code&gt;anvi-interactive&lt;/code&gt; command and accessory files that you want to after creating/uploading those files on Poseidon.&lt;/p&gt;

&lt;p&gt;Happy interacting!s&lt;/p&gt;
</description>
    </item>
    
    <item>
      <title>Bio-GO-SHIP: The Time Is Right to Establish Global Repeat Sections of Ocean Biology</title>
      <link>https://alexanderlabwhoi.github.io/publication/clayton-2022-bio/</link>
      <pubDate>Sat, 01 Jan 2022 00:00:00 -0500</pubDate>
      
      <guid>https://alexanderlabwhoi.github.io/publication/clayton-2022-bio/</guid>
      <description></description>
    </item>
    
    <item>
      <title>Marine microeukaryote metatranscriptomics: sample processing and bioinformatic workflow recommendations for ecological applications</title>
      <link>https://alexanderlabwhoi.github.io/publication/cohen-2022-marine/</link>
      <pubDate>Sat, 01 Jan 2022 00:00:00 -0500</pubDate>
      
      <guid>https://alexanderlabwhoi.github.io/publication/cohen-2022-marine/</guid>
      <description></description>
    </item>
    
    <item>
      <title>Microbiomes of bloom-forming Phaeocystis algae are stable and consistently recruited, with both symbiotic and opportunistic modes</title>
      <link>https://alexanderlabwhoi.github.io/publication/mars-2022-microbiomes/</link>
      <pubDate>Sat, 01 Jan 2022 00:00:00 -0500</pubDate>
      
      <guid>https://alexanderlabwhoi.github.io/publication/mars-2022-microbiomes/</guid>
      <description></description>
    </item>
    
    <item>
      <title>Bio-GO-SHIP: Linking marine biodiversity and biogeochemistry</title>
      <link>https://alexanderlabwhoi.github.io/project/biogoship/</link>
      <pubDate>Fri, 02 Jul 2021 15:15:49 -0400</pubDate>
      
      <guid>https://alexanderlabwhoi.github.io/project/biogoship/</guid>
      <description>&lt;p&gt;The &lt;a href=&#34;http://biogoship.org/&#34; target=&#34;_blank&#34;&gt;Bio-GO-SHIP&lt;/a&gt; program aims to integrate the latest biological observing technologies into the Global Ocean Ship-based Hydrographic Investigation Program (GO-SHIP, &lt;a href=&#34;http://go-ship.org/&#34; target=&#34;_blank&#34;&gt;http://go-ship.org/&lt;/a&gt;). GO-SHIP runs a global repeat-section effort, wherein reference sections that transect major ocean regions are sampled every decade to observe global changes. Bio-GO-SHIP measurements will include optical, flow cytometric, metagenomic and metatranscriptomic, and particulate sampling. Compared to previous global ocean sequencing efforts, Bio-GO-SHIP will sample biological parameters at high spatial and vertical resolution, with ‘omic samples being taken approximately every degree, or approximately 26.5km on average between samples. My group is focused on the collection, sequencing, and preliminary assembly data product curation of the ‘omic dataset in conjunction with Adam Martiny’s lab&amp;ndash; with my lab taking the lead on the eukaryotic component.&lt;/p&gt;

&lt;p&gt;&lt;em&gt;Funding for this project provided by NOAA and the Simons Foundation&lt;/em&gt;&lt;/p&gt;
</description>
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