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01/01: talks: Add slides for Bio-IT World talk.


From: Ricardo Wurmus
Subject: 01/01: talks: Add slides for Bio-IT World talk.
Date: Tue, 22 May 2018 17:15:56 -0400 (EDT)

rekado pushed a commit to branch master
in repository maintenance.

commit 4c53d96a8cfd8e2a226db5f553b8b4ddad92714c
Author: Ricardo Wurmus <address@hidden>
Date:   Tue Apr 24 10:34:44 2018 +0200

    talks: Add slides for Bio-IT World talk.
---
 talks/bio-it-world-2018/Makefile                   |   39 +
 talks/bio-it-world-2018/about.org                  |   10 +
 talks/bio-it-world-2018/admins-1.svg               |  704 +++
 talks/bio-it-world-2018/admins-2.svg               |  679 +++
 talks/bio-it-world-2018/admins-3.svg               |  652 +++
 talks/bio-it-world-2018/big-graph.svg              | 5971 ++++++++++++++++++++
 talks/bio-it-world-2018/demo.svg                   |  457 ++
 talks/bio-it-world-2018/docker-1.svg               |  556 ++
 talks/bio-it-world-2018/docker-2.svg               |  444 ++
 talks/bio-it-world-2018/docker-3.svg               |  469 ++
 talks/bio-it-world-2018/docker-4.svg               |  574 ++
 talks/bio-it-world-2018/docker-5.svg               |  701 +++
 talks/bio-it-world-2018/end.svg                    |  551 ++
 talks/bio-it-world-2018/functional1.svg            |  494 ++
 talks/bio-it-world-2018/functional1a.svg           |  378 ++
 talks/bio-it-world-2018/functional1b.svg           |  417 ++
 talks/bio-it-world-2018/functional2.svg            |  601 ++
 talks/bio-it-world-2018/gc-1.svg                   |  826 +++
 talks/bio-it-world-2018/gc-2.svg                   |  774 +++
 talks/bio-it-world-2018/gc-3.svg                   |  737 +++
 .../images/coreutils-bag-graph.dot                 |  997 ++++
 talks/bio-it-world-2018/paper.svg                  | 1038 ++++
 talks/bio-it-world-2018/paper2.svg                 | 1210 ++++
 talks/bio-it-world-2018/profile-0.svg              |  763 +++
 talks/bio-it-world-2018/profile-1.svg              |  853 +++
 talks/bio-it-world-2018/rollback.svg               |  854 +++
 talks/bio-it-world-2018/talk.2018-05-16.pdf        |  Bin 0 -> 1122065 bytes
 talks/bio-it-world-2018/title.svg                  |  304 +
 talks/bio-it-world-2018/use-developer-1.svg        |  576 ++
 talks/bio-it-world-2018/use-developer-2.svg        |  598 ++
 talks/bio-it-world-2018/use-developer-3.svg        |  554 ++
 talks/bio-it-world-2018/use-developer-4.svg        |  765 +++
 talks/bio-it-world-2018/use-manifest-1.svg         |  740 +++
 talks/bio-it-world-2018/use-manifest-2.svg         |  713 +++
 talks/bio-it-world-2018/use-profile.svg            |  405 ++
 talks/bio-it-world-2018/use-rewrite-input.svg      |  992 ++++
 talks/bio-it-world-2018/use-summary.svg            |  541 ++
 37 files changed, 27937 insertions(+)

diff --git a/talks/bio-it-world-2018/Makefile b/talks/bio-it-world-2018/Makefile
new file mode 100644
index 0000000..cc63800
--- /dev/null
+++ b/talks/bio-it-world-2018/Makefile
@@ -0,0 +1,39 @@
+SLIDES=\
+  title \
+  docker-1 docker-2 docker-3 docker-4 \
+  functional1a functional1b functional1 functional2 graph \
+  demo \
+  use-profile use-rewrite-input use-manifest-1 use-manifest-2 use-summary \
+  paper paper2 \
+  use-developer-1 use-developer-2 use-developer-3 use-developer-4 \
+  admins-1 admins-2 admins-3 \
+  end
+
+
+# Extra slides for which there is no time:
+# environment-modules (after "problem")
+
+BONUS=\
+  profile-0 profile-1 rollback profile-1 \
+  gc-1 gc-2 gc-3
+
+slides.pdf: $(addsuffix .pdf, ${SLIDES} ${BONUS})
+       gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -sOutputFile=$@ $^
+
+big-graph.svg: images/coreutils-bag-graph.dot
+       dot -Tsvg -Gratio=.7 -o big-graph.svg $^
+
+big-graph.pdf: big-graph.svg
+       inkscape -z --export-background="#232323ff" --export-dpi=300 
--export-pdf=$@ $<
+
+graph.pdf: big-graph.pdf
+       gs -o $@ \
+               -sDEVICE=pdfwrite \
+        -g1920x1080 \
+               -dFIXEDMEDIA \
+               -dPDFFitPage \
+               -dCompatibilityLevel=1.4 \
+               $^
+
+%.pdf: %.svg
+       inkscape -z --export-dpi=300 --export-pdf=$@ $<
diff --git a/talks/bio-it-world-2018/about.org 
b/talks/bio-it-world-2018/about.org
new file mode 100644
index 0000000..20ffa66
--- /dev/null
+++ b/talks/bio-it-world-2018/about.org
@@ -0,0 +1,10 @@
+#+TITLE: Reproducible Bioinformatics Software Management with GNU Guix
+#+AUTHOR: Ricardo Wurmus, System Administrator/Software Developer, 
Bioinformatics Platform, Max Delbrück Center for Molecular Medicine, Berlin
+
+#+Event: Bio-IT World Conference, Boston, MA
+#+Date: Wednesday, May 16, 16:30
+#+Duration: 25min + 5min questions
+
+* Abstract
+
+We will introduce functional package management with GNU Guix, demonstrate 
some of the benefits it enables for research, such as reproducible software 
deployment, workflow-specific profiles, and user-managed environments, and 
share our experiences with using GNU Guix for bioinformatics research at the 
Max Delbrück Center. Functional package management differs from other software 
management methodologies in that reproducibility is a primary goal. We will 
also compare the properties and gu [...]
diff --git a/talks/bio-it-world-2018/admins-1.svg 
b/talks/bio-it-world-2018/admins-1.svg
new file mode 100644
index 0000000..79242b2
--- /dev/null
+++ b/talks/bio-it-world-2018/admins-1.svg
@@ -0,0 +1,704 @@
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