Giuliaguidi patch 9

.github/workflows/deploy.yml

@@ -15,13 +15,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - name: Checkout code
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
     - name: Setup Ruby
-      uses: actions/setup-ruby@v1
+      uses: ruby/setup-ruby@v1
       with:
-        ruby-version: '2.7'
+        ruby-version: '2.7' # Not needed with a .ruby-version file
+    - run: bundle exec rake
     - name: Enable bundler cache
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: vendor/bundle
         key: ${{ runner.os }}-gems-${{ hashFiles('**/Gemfile.lock') }}

Gemfile

@@ -1,5 +1,6 @@
 source 'https://rubygems.org'
 group :jekyll_plugins do
+    gem 'rake'
     gem 'github-pages'
     gem 'jekyll'
     gem 'jekyll-email-protect'

_bibliography/papers.bib

@@ -1,70 +1,124 @@
----
----
+@article{guidi2020cloud,
+    title={{10 Years Later: Cloud Computing is Closing the Performance Gap}}, 
+    author={Guidi, Giulia and Ellis, Marquita and Bulu\c{c}, Ayd{\i}n and Yelick, Katherine and Culler, David},
+    journal={4th Workshop on Hot Topics in Cloud Computing Performance at the International Conference on Performance Engineering (ICPE) 2021.},
+    selected={true},
+    year={2021}
+}
+
+@article{burchard2023space,
+  keywords={paper},
+  title={{Space Efficient Sequence Alignment for SRAM-Based Computing: X-Drop on the Graphcore IPU}},
+  author={Burchard, Luk and Zhao, Max Xiaohang and Langguth, Johannes and Bulu{\c{c}}, Ayd{\i}n and Guidi, Giulia},
+  journal={International Conference for High Performance Computing, Networking, Storage, and Analysis (SC'23)},
+  selected={true},
+  year={2023}
+}
+
+@inproceedings{popovici2023simd,
+  keywords={paper},
+  title={{Designing Efficient SIMD Kernels for High-Performance Sequence Alignment}},
+  author={Popovici, Doru Thom and Awan, Muaaz Gul, and Guidi, Giulia and Egan, Rob and Hofmeyr, Steven and Oliker, Leonid and Yelick, Katherine},
+  booktitle={2023 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)},
+  year={2023},
+  organization={IEEE}
+}
+
+@article{selvitopi2022extreme,
+  keywords={paper},
+  title={{Extreme-Scale Many-Against-Many Protein Similarity Search}},
+  author={Selvitopi, Oguz and Ekanayake, Saliya and Guidi, Giulia and Awan, Muaaz, and Pavlopoulos, Georgios and Azad, Ariful and Kyrpides, Nikos and Oliker, Leonid and Yelick, Katherine and Bulu\c{c}, Ayd{\i}n},
+  journal={International Conference for High Performance Computing, Networking, Storage, and Analysis (SC'22)},
+  year={2022}
+}
+
+@inproceedings{guidiraulet2022,
+  keywords={paper},
+  title = {{Distributed-Memory Parallel Contig Generation for De Novo Long-Read Genome Assembly}},
+  author = {Guidi, Giulia and Raulet, Gabriel and Rokhsar, Daniel and Oliker, Leonid and Yelick, Katherine and Bulu\c{c}, Ayd{\i}n},
+  booktitle = {51th International Conference on Parallel Processing (ICPP)},
+  year = {2022},
+  address = {Bordeaux, France}
+}
+
+
+@misc{garcia2021buddi,
+      title={{BuDDI: A Declarative Bloom Language for CALM Programming}}, 
+      author={Garcia, Rolando and Guidi, Giulia},
+      year={2021},
+      eprint={2109.08192},
+      archivePrefix={arXiv},
+      primaryClass={cs.DC}
+}
 
-@string{aps = {American Physical Society,}}
+@inproceedings{guidi2021bella,
+  title={{BELLA: Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper}},
+  author={Guidi, Giulia and Ellis, Marquita and Rokhsar, Daniel and Yelick, Katherine and Bulu{\c{c}}, Ayd{\i}n},
+  booktitle={SIAM Conference on Applied and Computational Discrete Algorithms (ACDA21)},
+  year={2021}
+}
+
+@article{yelick2020parallelism,
+  title={{The parallelism motifs of genomic data analysis}},
+  author={Yelick, Katherine and Bulu{\c{c}}, Ayd{\i}n and Awan, Muaaz and Azad, Ariful and Brock, Benjamin and Egan, Rob and Ekanayake, Saliya and Ellis, Marquita and Georganas, Evangelos and Guidi, Giulia and others},
+  journal={Philosophical Transactions of the Royal Society A},
+  year={2020},
+  publisher={The Royal Society Publishing}
+}
 
-@book{einstein1956investigations,
-  title={Investigations on the Theory of the Brownian Movement},
-  author={Einstein, Albert},
-  year={1956},
-  publisher={Courier Corporation,}
+@inproceedings{dibellaicpp19,
+  title = {{diBELLA: Distributed Long Read to Long Read Alignment}},
+  author = {Ellis, Marquita and Guidi, Giulia and Bulu\c{c}, Ayd{\i}n and Oliker, Leonid and Yelick, Katherine},
+  booktitle = {48th International Conference on Parallel Processing (ICPP)},
+  year = {2019},
+  address = {Kyoto, Japan}
 }
 
-@article{einstein1950meaning,
-  abbr={AJP},
-  title={The meaning of relativity},
-  author={Einstein, Albert and Taub, AH},
-  journal={American Journal of Physics,},
-  volume={18},
-  number={6},
-  pages={403--404},
-  year={1950},
-  publisher={American Association of Physics Teachers,}
+@article{selvitopi2020distributed,
+  title={{Distributed Many-to-Many Protein Sequence Alignment using Sparse Matrices}},
+  author={Selvitopi, Oguz and Ekanayake, Saliya and Guidi, Giulia and Pavlopoulos, Georgios and Azad, Ariful and Bulu{\c{c}}, Ayd{\i}n},
+  journal={International Conference for High Performance Computing, Networking, Storage, and Analysis (SC'20)},
+  year={2020}
 }
 
-@article{PhysRev.47.777,
-  abbr={PhysRev},
-  title={Can Quantum-Mechanical Description of Physical Reality Be Considered Complete?},
-  author={Einstein, A. and Podolsky, B. and Rosen, N.},
-  abstract={In a complete theory there is an element corresponding to each element of reality. A sufficient condition for the reality of a physical quantity is the possibility of predicting it with certainty, without disturbing the system. In quantum mechanics in the case of two physical quantities described by non-commuting operators, the knowledge of one precludes the knowledge of the other. Then either (1) the description of reality given by the wave function in quantum mechanics is not complete or (2) these two quantities cannot have simultaneous reality. Consideration of the problem of making predictions concerning a system on the basis of measurements made on another system that had previously interacted with it leads to the result that if (1) is false then (2) is also false. One is thus led to conclude that the description of reality as given by a wave function is not complete.},
-  journal={Phys. Rev.,},
-  volume={47},
-  issue={10},
-  pages={777--780},
-  numpages={0},
-  year={1935},
-  month={May},
-  publisher=aps,
-  doi={10.1103/PhysRev.47.777},
-  url={http://link.aps.org/doi/10.1103/PhysRev.47.777},
-  html={https://journals.aps.org/pr/abstract/10.1103/PhysRev.47.777},
-  pdf={example_pdf.pdf},
-  selected={true}
+@inproceedings{guidi2020parallel,
+  title={{Parallel String Graph Construction and Transitive Reduction for De Novo Genome Assembly}},
+  author={Guidi, Giulia and Selvitopi, Oguz and Ellis, Marquita and Oliker, Leonid and Yelick, Katherine and Bulu{\c{c}}, Ayd{\i}n},
+  booktitle = {International Parallel and Distributed Processing Symposium (IPDPS)},
+  selected={true},
+  year = {2021}
 }
 
-@article{einstein1905molekularkinetischen,
-  title={{\"U}ber die von der molekularkinetischen Theorie der W{\"a}rme geforderte Bewegung von in ruhenden Fl{\"u}ssigkeiten suspendierten Teilchen},
-  author={Einstein, A.},
-  journal={Annalen der physik,},
-  volume={322},
-  number={8},
-  pages={549--560},
-  year={1905},
-  publisher={Wiley Online Library}
+@inproceedings{logan2020,
+  title = {{LOGAN: {H}igh-{P}erformance {GPU}-{B}ased {X}-{D}rop {L}ong-{R}ead {A}lignment}},
+  author = {Zeni, Alberto and Guidi, Giulia and Ellis, Marquita and Ding, Nan and Santambrogio, Marco D. and Hofmeyr, Steven and Bulu\c{c}, Ayd{\i}n and Oliker, Leonid and Yelick, Katherine},
+  booktitle = {International Parallel and Distributed Processing Symposium (IPDPS)},
+  year = {2020},
+  address = {New Orleans, LA, USA}
+}
+@inproceedings{di2017hugenomics,
+  title={{HUGenomics: A Support to Personalized Medicine Research}},
+  author={Di Tucci, Lorenzo and Guidi, Giulia and Notargiacomo, Sara and Cerina, Luca and Scolari, Alberto and Santambrogio, Marco D.},
+  booktitle={Research and Technologies for Society and Industry (RTSI), 2017 IEEE 3rd International Forum on},
+  pages={1--5},
+  year={2017},
+  organization={IEEE}
 }
 
-@article{einstein1905movement,
-  abbr={Ann. Phys.},
-  title={Un the movement of small particles suspended in statiunary liquids required by the molecular-kinetic theory 0f heat},
-  author={Einstein, A.},
-  journal={Ann. Phys.,},
-  volume={17},
-  pages={549--560},
-  year={1905}
+@inproceedings{guidi2016improve,
+  title={{On How to Improve FPGA-Based Systems Design Productivity via SDAccel}},
+  author={Guidi, Giulia and Reggiani, Enrico and Di Tucci, Lorenzo and Durelli, Gianluca and Blott, Michaela and Santambrogio, Marco D.},
+  booktitle={2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)},
+  pages={247--252},
+  year={2016},
+  organization={IEEE}
 }
 
-@article{einstein1905electrodynamics,
-  title={On the electrodynamics of moving bodies},
-  author={Einstein, A.},
-  year={1905}
+@inproceedings{guidi2016rtsi,
+  title={{ProFAX: a Hardware Acceleration of a Protein Folding Algorithm}},
+  author={Guidi, Giulia and Di Tucci, Lorenzo and Santambrogio, Marco D.},
+  booktitle={2016 IEEE 2nd International Forum on Research and Technologies for Society and Industry Leveraging a better tomorrow (RTSI)},
+  pages={204--209},
+  year={2016},
+  organization={IEEE}
 }

_config.yml

@@ -3,19 +3,19 @@
 # -----------------------------------------------------------------------------
 
 title: blank # the website title (if blank, full name will be used instead)
-first_name: You
-middle_name: R.
-last_name: Name
-email: [email protected]
+first_name: Giulia
+middle_name:
+last_name: Guidi, PhD
+email: [email protected]
 description: > # the ">" symbol means to ignore newlines until "footer_text:"
-  A simple, whitespace theme for academics. Based on [*folio](https://github.com/bogoli/-folio) design.
+#Giulia Guidi's personal website.
 footer_text: >
   Powered by <a href="http://jekyllrb.com/" target="_blank">Jekyll</a> with <a href="https://github.com/alshedivat/al-folio">al-folio</a> theme.
   Hosted by <a href="https://pages.github.com/" target="_blank">GitHub Pages</a>.
   Photos from <a href="https://unsplash.com" target="_blank">Unsplash</a>.
 
-url:  # the base hostname & protocol for your site
-baseurl: /al-folio # the subpath of your site, e.g. /blog/
+url:     # the base hostname & protocol for your site
+baseurl: # the subpath of your site, e.g. /blog/
 last_updated: false # set to true if you want to display last updated in the footer
 impressum_path:  # set to path to include impressum link in the footer, use the same path as permalink in a page, helps to conform with EU GDPR
 
@@ -42,40 +42,40 @@ og_image: # The site-wide (default for all links) Open Graph preview image
 # Social integration
 # -----------------------------------------------------------------------------
 
-github_username: # your GitHub user name
-twitter_username: # your Twitter handle
-linkedin_username: # your LinkedIn user name
-scholar_userid: # your Google Scholar ID
+twitter_username: giuliaguidi
+github_username:  giuliaguidi   # your GitHub user name
+linkedin_username: giulia-guidi # your LinkedIn user name
+scholar_userid: UZLC4TYAAAAJ # your Google Scholar ID
 orcid_id: # your ORCID ID
 medium_username: # your Medium username
 quora_username: # your Quora username
 publons_id: # your ID on Publons
-research_gate_profile: # your profile on ResearchGate
+research_gate_profile: # research gate profile
 blogger_url: # your blogger URL
 work_url: # work page URL
 keybase_username: # your keybase user name
 wikidata_id: # your wikidata id
 
 contact_note: >
-  You can even add a little note about which of these is the best way to reach you.
+  The best way to contact me is via email.
 
-google_analytics: UA-XXXXXXXXX # out your google-analytics code
+google_analytics: # out your google-analytics code 
 panelbear_analytics: XXXXXXXXX # panelbear analytics site ID
 
 # -----------------------------------------------------------------------------
 # Blog
 # -----------------------------------------------------------------------------
 
-blog_name: al-folio  # your blog must have a name for it to show up in the nav bar
-blog_description: a simple whitespace theme for academics
-permalink: /blog/:year/:title/
+# blog_name: gguidi  # your blog must have a name for it to show up in the nav bar
+# blog_description: a simple whitespace theme for academics
+# permalink: /blog/:year/:title/
 
 # Pagination
 pagination:
   enabled: true
 
 # Comments
-disqus_shortname: al-folio # put your disqus shortname
+disqus_shortname: gguidi # put your disqus shortname
 
 # -----------------------------------------------------------------------------
 # Collections
@@ -91,7 +91,7 @@ collections:
     output: true
     permalink: /projects/:path/
 
-news_limit: 5
+news_limit: 8
 
 # -----------------------------------------------------------------------------
 # Jekyll settings
@@ -138,8 +138,8 @@ plugins:
 
 scholar:
 
-  last_name: Einstein
-  first_name: [Albert, A.]
+  last_name: Guidi
+  first_name: [Giulia, G.]
 
   style: apa
   locale: en
@@ -166,7 +166,7 @@ enable_panelbear_analytics: false
 enable_mansory:             true
 enable_math:                true
 enable_tooltips:            false
-enable_darkmode:            true
+enable_darkmode:            false
 show_social_icons:          false
 
 # -----------------------------------------------------------------------------

_data/coauthors.yml

@@ -1,18 +1,39 @@
-"Adams":
-  - firstname: ["Edwin", "E.", "E. P.", "Edwin Plimpton"]
-    url: https://en.wikipedia.org/wiki/Edwin_Plimpton_Adams
+"Buluç":
+  - firstname: ["Aydın", "A."]
+    url: http://people.eecs.berkeley.edu/~aydin/
 
-"Podolsky":
-  - firstname: ["Boris", "B.", "B. Y.", "Boris Yakovlevich"]
-    url: https://en.wikipedia.org/wiki/Boris_Podolsky
+"Garcia":
+  - firstname: ["Rolando", "R."]
+    url: https://rlnsanz.github.io/
 
-"Rosen":
-  - firstname: ["Nathan", "N."]
-    url: https://en.wikipedia.org/wiki/Nathan_Rosen
+"Yelick":
+  - firstname: ["Katherine", "K."]
+    url: https://en.wikipedia.org/wiki/Katherine_Yelick
 
-"Bach": 
-  - firstname: ["Johann Sebastian", "J. S."]
-    url: https://en.wikipedia.org/wiki/Johann_Sebastian_Bach
+"Ellis":
+  - firstname: ["Marquita", "M."]
+    url: https://sites.google.com/view/about-mme
 
-  - firstname: ["Carl Philipp Emanuel", "C. P. E."]
-    url: https://en.wikipedia.org/wiki/Carl_Philipp_Emanuel_Bach
+"Culler": 
+  - firstname: ["David", "D."]
+    url: https://en.wikipedia.org/wiki/David_Culler
+
+"Di Tucci":
+  - firstname: ["Lorenzo", "L."]
+    url: https://www.linkedin.com/in/lorenzoditucci/
+
+"Santambrogio":
+  - firstname: ["Marco", "M.", "Marco Domenico", "M. D."]
+    url: https://www.deib.polimi.it/eng/people/details/356156
+
+"Selvitopi":
+  - firstname: ["Oguz", "O."]
+    url: https://crd.lbl.gov/departments/computer-science/par/members/staff/oguz-selvitopi/
+
+"Oliker":
+  - firstname: ["Leonid", "L."]
+    url: https://crd.lbl.gov/departments/computer-science/par/members/group-lead/leonid-oliker/
+
+"Rokhsar":
+  - firstname: ["Daniel", "D."]
+    url: http://mcb.berkeley.edu/faculty/all/rokhsard

_includes/head.html

@@ -25,7 +25,9 @@
 <link rel="stylesheet" type="text/css" href="https://fonts.googleapis.com/css?family=Roboto:300,400,500,700|Roboto+Slab:100,300,400,500,700|Material+Icons">
 
 <!-- Code Syntax Highlighting -->
-<link rel="stylesheet" href="https://gitcdn.link/repo/jwarby/jekyll-pygments-themes/master/{{ site.highlight_theme }}.css" />
+<!-- <link rel="stylesheet" href="https://gitcdn.link/repo/jwarby/jekyll-pygments-themes/master/{{ site.highlight_theme }}.css" />
+ -->
+<link rel="stylesheet" href="https://combinatronics.io/jwarby/pygments-css/master/{{ site.highlight_theme }}.css" />
 
 <!-- Styles -->
 <link rel="shortcut icon" href="{{ '/assets/img/favicon.ico' | relative_url }}">

_news/announcement_1.md

@@ -1,7 +1,7 @@
 ---
 layout: post
-date: 2015-10-22 15:59:00-0400
+date: 2020-07-31 11:00:00-0400
 inline: true
 ---
 
-A simple inline announcement.
+I'm happy to annouce that I have been selected as [2020 SIGHPC Computational & Data Science Fellow](https://www.sighpc.org/for-your-career/fellowships/2020-fellowship-winners?fbclid=IwAR2N8swtCYgNH3phRmrFtASSC42b4oN5joG1l5XHFSdnkMY6U4HvZt3olLE).

_news/announcement_10.md

@@ -0,0 +1,7 @@
+---
+layout: post
+date: 2021-08-18 11:00:00-0400
+inline: true
+---
+
+I'm very happy I had the opportunity to give the first [in-person seminar](https://memento.epfl.ch/event/ic-talk-sparse-matrices-and-high-performance-com-2/) in more than 1y at [EPFL IC](https://www.epfl.ch/schools/ic/) entitled ["Sparse Matrices and High-Performance Computing Meet Biology"](https://drive.google.com/file/d/1jyBMo7sN5qmlKJG6UETAHOPU8u8iyKIC/view).