<html><head><style>body{font-family:Avenir,Arial;font-size:13px}</style></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div id="bloop_customfont" style="font-family:Avenir,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Titus, </div><div id="bloop_customfont" style="font-family:Avenir,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div><div id="bloop_customfont" style="font-family:Avenir,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">So much of your ethos is centered on “Open Science”. It would be nice to see this featured in the “khmer is" mission statement. E.g. Khmer is: an open source platform for.. In my mind, this is more than a goal, instead this is a core value that underpins the entire project. </div><div id="bloop_customfont" style="font-family:Avenir,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div><div id="bloop_customfont" style="font-family:Avenir,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">My 2 cents, </div><div id="bloop_customfont" style="font-family:Avenir,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Matt</div> <div id="bloop_sign_1416087528845943040" class="bloop_sign"><div style="font-family:helvetica,arial;font-size:13px"><span style="line-height: normal; font-size: 8.5pt; font-family: Avenir, serif; color: rgb(0, 0, 153);">______________________________________________<br><b>Matthew MacManes, Ph.D.</b><br>University of New Hampshire I Assistant Professor of Genome Enabled Biology<br>Department of Molecular, Cellular, & Biomedical Sciences<br>Durham, NH 03824<br></span><span style="font-size: 10pt; line-height: normal; font-family: Helvetica, sans-serif;"><a href="tel://Phone:%20603-862-4052" style="color: purple;"><span style="font-size: 8.5pt; font-family: Avenir, serif;">Phone: 603-862-4052</span></a></span><span style="line-height: normal; font-size: 8.5pt; font-family: Avenir, serif; color: rgb(0, 0, 153);"> I Twitter: </span><span style="font-size: 10pt; line-height: normal; font-family: Helvetica, sans-serif;"><a href="https://twitter.com/PeroMHC" style="color: purple;"><span style="font-size: 8.5pt; font-family: Avenir, serif;">@PeroMHC</span></a></span><span style="line-height: normal; font-size: 8.5pt; font-family: Avenir, serif; color: rgb(0, 0, 153);"> | Web: </span><span style="font-size: 10pt; line-height: normal; font-family: Helvetica, sans-serif;"><a href="http://genomebio.org/" style="color: purple;"><span style="font-size: 8.5pt; font-family: Avenir, serif;">genomebio.org</span></a></span><span style="line-height: normal; font-size: 8.5pt; font-family: Avenir, serif; color: rgb(0, 0, 153);"><br>Office: 189 Rudman Hall | Laboratory: 145 Rudman Hall</span></div></div> <br><p style="color:#000;">On November 15, 2014 at 9:55:16 AM, C. Titus Brown (<a href="mailto:ctb@msu.edu">ctb@msu.edu</a>) wrote:</p> <blockquote type="cite" class="clean_bq"><span><div><div></div><div>Hi all,
<br>
<br>as we think about the next few years of khmer development, I think it is helpful to explore what khmer is, roughly speaking, and what our goals should be.
<br>
<br>Here’s a rough cut; I’d like to turn this into a blog post, but only after some feedback from the list (if any).
<br>
<br>----
<br>
<br>khmer is:
<br>
<br>* a stable research platform for novel CS/bio research on data structures and algorithms, mostly k-mer based;
<br>* a test bed for software engineering practice in science;
<br>* a Python library for working with k-mers and graph structures;
<br>* an exercise in community building in scientific software engineering;
<br>* an exercise in ecosystem participation in scientific software engineering;
<br>
<br>----
<br>
<br>khmer long term goals, in some rough order of priority:
<br>
<br>* Keep khmer versatile and agile enough to easily enable the CS and bio we want to do. Practical implications: limit complexity of internals as much as possible.
<br>
<br>* Continue community building. Practical implications: run khmer as a real open source project, with everything done in the open; work nicely with other projects.
<br>
<br>* Build, sustain, and maintain a set of protocols and recipes around khmer. Practical implications: take workflow design into account.
<br>
<br>* Improve the efficiency (time/memory) of khmer implementations. Practical implications: optimize, but not at expense of clean code. Some specifics: streaming; variable sized counters.
<br>
<br>* Lower barriers to an increasing user base. Practical implications: find actual pain points, address if it’s easy or makes good sense. Some specifics: hash function k > 32, stranded hash function, integrate efficient k-mer cardinality counting, implement dynamically sized data structures.
<br>
<br>* Keep khmer technologically up to date. Practical implications: transition to Python 3.
<br>
<br>——
<br>
<br>Thoughts? What am I missing? What should be added or changed?
<br>
<br>cheers,
<br>—titus
<br>
<br>
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