15 files changed, 579 insertions, 0 deletions
diff --git a/content/_index.md b/content/_index.md
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++++
+title = "About"
++++
+
+I'm a PhD student at the University of Coimbra and University of Lille
+under a co-tutelle program advised by [Luís
+Paquete](https://eden.dei.uc.pt/~paquete), [Arnaud
+Liefooghe](https://sites.google.com/site/arnaudliefooghe/) and [Bilel
+Derbel](https://sites.google.com/site/bilelderbelpro/). I'm also
+working as an Invited Assistant at the University of Coimbra, part of
+the [ALGO](https://algo.dei.uc.pt/) research lab, and a member of the
+[TOPDEI](https://top.dei.uc.pt) project that is preparing students for
+programming competitions. Previously, I worked as a full stack
+developer at [Whitesmith](https://whitesmith.co).
+
+Research-wise I'm mainly interested in Multi-Objective Optimization,
+Combinatorial Optimization, Anytime Algorithms, Automated Algorithm
+Selection, Automated Algorithm Configuration, and Reproducibility. I
+am also moderately interested in Compilers, Distributed Computing, and
+High-Performance Computing (HPC).
+
+Technology-wise I'm mainly working with Linux, Emacs, C/C++, Rust, R,
+Python, Nix, GLPK, Slurm, and SQLite.
+
+### Email
+
+- Personal: [public@adbjesus.com](mailto:public@adbjesus.com)
+- Professional: [ajesus@dei.uc.pt](mailto:ajesus@dei.uc.pt)
+
+Please [use plaintext](https://useplaintext.email/) when contacting
+me.
+
+### Around the Web
+
+* [ORCID](https://orcid.org/0000-0001-7691-0295)
+* [Scholar](https://scholar.google.com/citations?user=D2me-IYAAAAJ&hl=en)
+* [Research Gate](https://www.researchgate.net/profile/Alexandre_Jesus2)
+* [Github](https://github.com/adbjesus)
+
+
diff --git a/content/blog/01-hello-world/index.md b/content/blog/01-hello-world/index.md
new file mode 100644
index 0000000..e0aaefe
--- /dev/null
+++ b/content/blog/01-hello-world/index.md
@@ -0,0 +1,193 @@
+---
+author: A.D.B. Jesus
+date: 2022-08-29
+slug: hello-world
+title: Hello, world!
+---
+
+I have been thinking of starting a blog for a while, mostly to write
+about stuff that makes no sense to publish academically, but also to
+improve my writing skills. I expect to mostly write about Programming,
+Emacs, Linux, and other tech topics. But we will see where it goes.
+
+In this first post I will quickly go over the implementation and
+deployment of this site. Note that, you can find the code for this site
+at <https://git.adbjesus.com/website>.
+
+### Static Site Generator
+
+Since this site will contain static content, I've decided to go with a
+static site generator. In particular, I chose
+[Zola](https://getzola.org). The main reason for using Zola and not
+something else is that I am familiar with its implementation language
+(Rust). This can allow me to easily contribute to the project to fix any
+issue or scratch any itch.
+
+In terms of styling, I'm using simple templates and CSS I implemented
+myself, which match the light/dark system theme option set by the user.
+Something I am not yet doing, is using syntax highlighting for code in
+blog posts. Although Zola supports this, it does not support some of the
+languages that I want, such as Emacs Lisp and Nix, and it is using old
+and buggy Sublime syntaxes. There is currently an [open
+issue](https://github.com/getzola/zola/issues/1787) to replace the
+current system. Another option, would be to use a javascript based
+syntax highlighter. However, I would rather keep my site
+javascript-free. As a result, since I don't consider it to be a critical
+feature for now, I will not implement any syntax highlighting for the
+time being.
+
+### Using Org
+
+One issue I had with Zola is that it does not suppor
+[Org](https://orgmode.org) for writing content (see this
+[issue](https://github.com/getzola/zola/issues/909)). However, I would
+prefer to use it instead of markdown because I prefer and am more
+comfortable with its syntax, but also because I want to be able to use
+[Org Babel](https://orgmode.org/worg/org-contrib/babel/) to execute code
+within the `.org` file directly when writing posts for which executing
+code is useful.
+
+Nonetheless, this proved not to be an issue for my simple use case
+because I can automatically convert `.org` files to `.md` files
+(following the [CommonMark](https://commonmark.org/) spec) using
+[pandoc](https://pandoc.org), and the
+[ox-pandoc](https://github.com/emacsorphanage/ox-pandoc) package for
+Emacs. To setup ox-pandoc to export `.org` files to CommonMark I have
+the following in my Emacs configuration:
+
+``` elisp
+(use-package ox-pandoc
+  :ensure t
+  :after org
+  :custom
+  (org-pandoc-menu-entry
+   '((?c "to cmk." org-pandoc-export-to-commonmark)
+     (?C "to cmk and open." org-pandoc-export-to-commonmark-and-open))))
+```
+
+Then, I put the `index.org` for a blog post inside a dedicated folder
+for that post:
+
+``` example
+content
+└── blog
+   └── 01-hello-world
+      ├── index.org
+      └── ... // other files
+```
+
+The `index.org` file includes some metadata in its header for both Zola
+and ox-pandoc. For example, for this post I'm using the following
+header:
+
+``` org
+#+TITLE: Hello, world!
+#+DATE: 2022-08-25
+#+PANDOC_METADATA: slug:hello-world
+#+PANDOC_EXTENSIONS: commonmark+yaml_metadata_block
+#+PANDOC_OPTIONS: standalone:t
+#+PANDOC_OPTIONS: shift-heading-level-by:2
+```
+
+The `TITLE`, `DATE`, and `PANDOC_METADATA` fields are added to the
+exported markdown metadata block. To add the metadata block to the
+generated markdown file we set the `yaml_metadata_block` pandoc
+extension in `PANDOC_EXTENSIONS`, and the `standalone:t` option in
+`PANDOC_OPTIONS`. The last line is used to start the generated headings'
+levels at 3 for styling purposes.
+
+Finally, I use the `C-c C-e p c` shortcut to generate the markdown file,
+which goes into the same folder, i.e.:
+
+``` example
+content
+└── blog
+   └── 01-hello-world
+      ├── index.org
+      ├── index.md
+      └── ... // other files
+```
+
+You can find the Org source for this post [here](index.org).
+
+### Deploying with Nix
+
+I deploy this site to my [NixOS](https://nixos.org) server using the
+declarative NixOS configuration capabilities. For this I have a
+`flake.nix` in the repository of this site:
+
+``` nix
+{
+  description = "My personal website";
+
+  inputs = {
+    nixpkgs = {
+      url = "github:nixos/nixpkgs/nixos-22.05";
+    };
+
+    flake-utils = {
+      url = "github:numtide/flake-utils";
+      inputs.nixpkgs.follows = "nixpkgs";
+    };
+  };
+
+  outputs = { self, nixpkgs, flake-utils }:
+    flake-utils.lib.eachDefaultSystem (system:
+      let
+        pkgs = import nixpkgs { inherit system; };
+      in rec {
+        packages.website =
+          pkgs.stdenv.mkDerivation {
+            name = "website";
+            src = self;
+
+            buildInputs = [ pkgs.zola ];
+
+            buildPhase = ''
+              zola build
+            '';
+
+            installPhase = ''
+              mkdir -p $out cp -Tr public $out/public
+            '';
+          };
+
+        packages.default = self.packages.${system}.website;
+      }
+    );
+}
+```
+
+Then I add this repository to the inputs section of the NixOS
+`flake.nix` configuration file.
+
+``` nix
+inputs.website = {
+  url = "git+https://git.adbjesus.com/website";
+  inputs.nixpkgs.follows = "nixpkgs";
+};
+```
+
+and use the `nginx.virtualHosts` option to deploy it:
+
+``` nix
+nginx.virtualHosts = {
+  "adbjesus.com" = {
+    default = true;
+    forceSSL = true;
+    enableACME = true;
+    locations = {
+      "/" = {
+        root = "${inputs.website.packages.${system}.website}/public";
+        extraConfig = ''
+          add_header Last-Modified "${toDateTime inputs.website.lastModified}";
+          add_header Cache-Control max-age="${toString (60 * 60 * 24)}";
+        '';
+      };
+    };
+  };
+};
+```
+
+In the future, I will write more about my NixOS configuration using
+flakes, which I use to manage my personal computers and server.
diff --git a/content/blog/01-hello-world/index.org b/content/blog/01-hello-world/index.org
new file mode 100644
index 0000000..aa51773
--- /dev/null
+++ b/content/blog/01-hello-world/index.org
@@ -0,0 +1,190 @@
+#+TITLE: Hello, world!
+#+DATE: 2022-08-29
+#+AUTHOR: A.D.B. Jesus
+#+PANDOC_METADATA: slug:hello-world
+#+PANDOC_EXTENSIONS: commonmark+yaml_metadata_block
+#+PANDOC_OPTIONS: standalone:t
+#+PANDOC_OPTIONS: shift-heading-level-by:2
+#+SPDX-FileCopyrightText: 2022 A.D.B. Jesus <https://adbjesus.com>
+#+SPDX-License-Identifier: CC-BY-SA-4.0
+
+I have been thinking of starting a blog for a while, mostly to write
+about stuff that makes no sense to publish academically, but also to
+improve my writing skills. I expect to mostly write about Programming,
+Emacs, Linux, and other tech topics. But we will see where it goes.
+
+In this first post I will quickly go over the implementation and
+deployment of this site. Note that, you can find the code for this
+site at https://git.adbjesus.com/website.
+
+* Static Site Generator
+
+Since this site will contain static content, I've decided to go with a
+static site generator. In particular, I chose [[https://getzola.org][Zola]]. The main reason
+for using Zola and not something else is that I am familiar with its
+implementation language (Rust). This can allow me to easily contribute
+to the project to fix any issue or scratch any itch.
+
+In terms of styling, I'm using simple templates and CSS I implemented
+myself, which match the light/dark system theme option set by the
+user. Something I am not yet doing, is using syntax highlighting for
+code in blog posts. Although Zola supports this, it does not support
+some of the languages that I want, such as Emacs Lisp and Nix, and it
+is using old and buggy Sublime syntaxes. There is currently an [[https://github.com/getzola/zola/issues/1787][open
+issue]] to replace the current system. Another option, would be to use a
+javascript based syntax highlighter. However, I would rather keep my
+site javascript-free. As a result, since I don't consider it to be a
+critical feature for now, I will not implement any syntax highlighting
+for the time being.
+
+* Using Org
+
+One issue I had with Zola is that it does not suppor [[https://orgmode.org][Org]] for writing
+content (see this [[https://github.com/getzola/zola/issues/909][issue]]). However, I would prefer to use it instead of
+markdown because I prefer and am more comfortable with its syntax, but
+also because I want to be able to use [[https://orgmode.org/worg/org-contrib/babel/][Org Babel]] to execute code within
+the =.org= file directly when writing posts for which executing code
+is useful.
+
+Nonetheless, this proved not to be an issue for my simple use case
+because I can automatically convert =.org= files to =.md= files
+(following the [[https://commonmark.org/][CommonMark]] spec) using [[https://pandoc.org][pandoc]], and the [[https://github.com/emacsorphanage/ox-pandoc][ox-pandoc]]
+package for Emacs. To setup ox-pandoc to export =.org= files to
+CommonMark I have the following in my Emacs configuration:
+
+#+begin_src elisp :eval no
+(use-package ox-pandoc
+  :ensure t
+  :after org
+  :custom
+  (org-pandoc-menu-entry
+   '((?c "to cmk." org-pandoc-export-to-commonmark)
+     (?C "to cmk and open." org-pandoc-export-to-commonmark-and-open))))
+#+end_src
+
+Then, I put the =index.org= for a blog post inside a dedicated folder
+for that post:
+
+#+begin_example
+content
+└── blog
+   └── 01-hello-world
+      ├── index.org
+      └── ... // other files
+#+end_example
+
+The =index.org= file includes some metadata in its header for both
+Zola and ox-pandoc. For example, for this post I'm using the following
+header:
+
+#+begin_src org :eval no
+#+TITLE: Hello, world!
+#+DATE: 2022-08-25
+#+PANDOC_METADATA: slug:hello-world
+#+PANDOC_EXTENSIONS: commonmark+yaml_metadata_block
+#+PANDOC_OPTIONS: standalone:t
+#+PANDOC_OPTIONS: shift-heading-level-by:2
+#+end_src
+
+The =TITLE=, =DATE=, and =PANDOC_METADATA= fields are added to the
+exported markdown metadata block. To add the metadata block to the
+generated markdown file we set the =yaml_metadata_block= pandoc
+extension in =PANDOC_EXTENSIONS=, and the =standalone:t= option in
+=PANDOC_OPTIONS=. The last line is used to start the generated
+headings' levels at 3 for styling purposes.
+
+Finally, I use the =C-c C-e p c= shortcut to generate the markdown file,
+which goes into the same folder, i.e.:
+
+#+begin_example
+content
+└── blog
+   └── 01-hello-world
+      ├── index.org
+      ├── index.md
+      └── ... // other files
+#+end_example
+
+You can find the Org source for this post [[file:index.org][here]].
+
+* Deploying with Nix
+
+I deploy this site to my [[https://nixos.org][NixOS]] server using the declarative NixOS
+configuration capabilities. For this I have a =flake.nix= in the
+repository of this site:
+
+#+begin_src nix
+{
+  description = "My personal website";
+
+  inputs = {
+    nixpkgs = {
+      url = "github:nixos/nixpkgs/nixos-22.05";
+    };
+
+    flake-utils = {
+      url = "github:numtide/flake-utils";
+      inputs.nixpkgs.follows = "nixpkgs";
+    };
+  };
+
+  outputs = { self, nixpkgs, flake-utils }:
+    flake-utils.lib.eachDefaultSystem (system:
+      let
+        pkgs = import nixpkgs { inherit system; };
+      in rec {
+        packages.website =
+          pkgs.stdenv.mkDerivation {
+            name = "website";
+            src = self;
+
+            buildInputs = [ pkgs.zola ];
+
+            buildPhase = ''
+              zola build
+            '';
+
+            installPhase = ''
+              mkdir -p $out cp -Tr public $out/public
+            '';
+          };
+
+        packages.default = self.packages.${system}.website;
+      }
+    );
+}
+#+end_src
+
+Then I add this repository to the inputs section of the NixOS
+=flake.nix= configuration file.
+
+#+begin_src nix
+inputs.website = {
+  url = "git+https://git.adbjesus.com/website";
+  inputs.nixpkgs.follows = "nixpkgs";
+};
+#+end_src
+
+and use the =nginx.virtualHosts= option to deploy it:
+
+#+begin_src nix
+nginx.virtualHosts = {
+  "adbjesus.com" = {
+    default = true;
+    forceSSL = true;
+    enableACME = true;
+    locations = {
+      "/" = {
+        root = "${inputs.website.packages.${system}.website}/public";
+        extraConfig = ''
+          add_header Last-Modified "${toDateTime inputs.website.lastModified}";
+          add_header Cache-Control max-age="${toString (60 * 60 * 24)}";
+        '';
+      };
+    };
+  };
+};
+#+end_src
+
+In the future, I will write more about my NixOS configuration using
+flakes, which I use to manage my personal computers and server.
diff --git a/content/blog/_index.md b/content/blog/_index.md
new file mode 100644
index 0000000..e6aaf2f
--- /dev/null
+++ b/content/blog/_index.md
@@ -0,0 +1,6 @@
++++
+title = "Blog"
+sorted_by = "date"
+template = "blog.html"
+generate_feed = true
++++
diff --git a/content/publications/dias2021nondlib.pdf b/content/publications/dias2021nondlib.pdf
new file mode 100644
index 0000000..8a3a888
--- /dev/null
+++ b/content/publications/dias2021nondlib.pdf
diff --git a/content/publications/index.md b/content/publications/index.md
new file mode 100644
index 0000000..df1f564
--- /dev/null
+++ b/content/publications/index.md
@@ -0,0 +1,61 @@
++++
+title = "Publications"
++++
+
+### Journal Articles
+
+- **A. D. Jesus**, L. Paquete, and A. Liefooghe, &ldquo;A model of
+  anytime algorithm performance for bi-objective optimization&rdquo;,
+  _Journal of Global Optimization_, vol. 79, pp. 329–350, Feb. 2021.
+  [DOI](https://doi.org/10.1007/s10898-020-00909-9) ::
+  [PDF](jesus2020model.pdf)
+- **A. D. Jesus**, L. Paquete, and J. R. Figueira. &ldquo;Finding
+  representations for an unconstrained bi-objective combinatorial
+  optimization problem&rdquo;, _Optimization Letters_, vol. 12, pp.
+  321-334, March 2018.
+  [DOI](https://doi.org/10.1007/s11590-017-1129-6) ::
+  [PDF](jesus2018finding.pdf)
+
+### Conference Articles
+
+- **A. D. Jesus**, L. Paquete, B. Derbel, and A. Liefooghe, &ldquo;On
+  the design and anytime performance of indicator-based branch and
+  bound for multi-objective combinatorial optimization&rdquo;, in
+  _Proceedings of the 2021 Genetic and Evolutionary Computation
+  Conference (GECCO '21)_, pp. 234-242, June 2021.
+  [DOI](https://doi.org/10.1145/3449639.3459360) ::
+  [PDF](jesus2021design.pdf)
+- **A. D. Jesus**, A. Liefooghe, B. Derbel, and L. Paquete,
+  &ldquo;Algorithm Selection of Anytime Algorithms&rdquo;, in
+  _Proceedings of the 2020 Genetic and Evolutionary Computation
+  Conference (GECCO '20)_, pp. 850-858, June 2020.
+  [DOI](https://doi.org/10.1145/3377930.3390185) ::
+  [PDF](jesus2020algorithm.pdf)
+
+### (Extended) Abstracts
+
+- **A. D. Jesus**, L. Paquete, A. Liefooghe, and B. Derbel,
+  &ldquo;Techniques to analyze the anytime behavior of algorithms for
+  multi-objective optimization&rdquo;, in _31st European Conference on
+  Operational Research (EURO 2021)_, July 2021.
+  [PDF](jesus2021techniques.pdf)
+- D. M. Dias, **A. D. Jesus**, and L. Paquete, &ldquo;A software
+  library for archiving nondominated points&rdquo;, in _Proceedings of
+  the 2021 Genetic and Evolutionary Computation Conference Companion
+  (GECCO '21)_, pp. 53-54, June 2021.
+  [DOI](https://doi.org/10.1145/3449726.3462737) ::
+  [PDF](dias2021nondlib.pdf)
+- **A. D. Jesus**, L. Paquete, A. Liefooghe. &ldquo;A model of anytime
+  algorithm performance for biobjective optimization problems&rdquo;,
+  in _Proceedings of the 14th International Global Optimization
+  Workshop (LeGO 2018)_, AIP Conference Proceedings 2070(1),
+  p. 020049, Feb. 2019. [DOI](https://doi.org/10.1063/1.5090016) ::
+  [PDF](jesus2019model.pdf)
+
+### Theses
+
+- **A. D. B. Jesus**, &ldquo;Implicit Enumeration for Representation
+  Systems in Multi-objective Optimization&rdquo;, MSc thesis,
+  University of Coimbra, Sep. 2015.
+  [Handle](https://hdl.handle.net/10316/35604) ::
+  [PDF](jesus2015implicit.pdf)
diff --git a/content/publications/jesus2015implicit.pdf b/content/publications/jesus2015implicit.pdf
new file mode 100644
index 0000000..36b9309
--- /dev/null
+++ b/content/publications/jesus2015implicit.pdf
diff --git a/content/publications/jesus2018finding.pdf b/content/publications/jesus2018finding.pdf
new file mode 100644
index 0000000..4474004
--- /dev/null
+++ b/content/publications/jesus2018finding.pdf
diff --git a/content/publications/jesus2019model.pdf b/content/publications/jesus2019model.pdf
new file mode 100644
index 0000000..35bcccc
--- /dev/null
+++ b/content/publications/jesus2019model.pdf
diff --git a/content/publications/jesus2020algorithm.pdf b/content/publications/jesus2020algorithm.pdf
new file mode 100644
index 0000000..baa70bd
--- /dev/null
+++ b/content/publications/jesus2020algorithm.pdf
diff --git a/content/publications/jesus2020model.pdf b/content/publications/jesus2020model.pdf
new file mode 100644
index 0000000..29bd249
--- /dev/null
+++ b/content/publications/jesus2020model.pdf
diff --git a/content/publications/jesus2021design.pdf b/content/publications/jesus2021design.pdf
new file mode 100644
index 0000000..532b6ad
--- /dev/null
+++ b/content/publications/jesus2021design.pdf
diff --git a/content/publications/jesus2021techniques.pdf b/content/publications/jesus2021techniques.pdf
new file mode 100644
index 0000000..1575e10
--- /dev/null
+++ b/content/publications/jesus2021techniques.pdf
diff --git a/content/software/index.md b/content/software/index.md
new file mode 100644
index 0000000..045624e
--- /dev/null
+++ b/content/software/index.md
@@ -0,0 +1,58 @@
++++
+title = "Software"
++++
+
+### mooutils
+
+  C++ library containing several utilities to aid in the
+  implementation of multi-objective optimization algorithms, such as:
+  quality indicators, dominance relations, sets of non-dominated
+  points/solutions, queues of solutions.
+
+  [Github](https://github.com/adbjesus/mooutils),
+  [Zenodo](https://doi.org/10.5281/zenodo.6855878)
+
+### mobkp
+
+  C++ library and solver for the multi-objective binary knapsack
+  problem, which includes several state of the art algorithms.
+
+  [Github](https://github.com/adbjesus/mobkp),
+  [Zenodo](https://doi.org/10.5281/zenodo.6857685)
+
+### anytime
+
+  R library to help analyze the anytime behavior of algorithms, which
+  provides several publication ready `ggplot2` plots, and a scalar
+  measure of anytime performance.
+
+  [Github](https://github.com/adbjesus/anytime),
+  [Zenodo](https://doi.org/10.5281/zenodo.6856119)
+
+### nondLib
+
+  C++ library for building and updatings sets of nondominated points,
+  providing several methods to filter the nondominated points from a
+  larger set, and a method to add nondominated points to a set.
+
+  [Github](https://github.com/TLDart/nondLib),
+  [Zenodo](https://doi.org/10.5281/zenodo.4733026)
+
+### apm
+
+  C++ library and binary for computing models of anytime
+  performance. Currently, it supports a theoretical model of anytime
+  performance for bi-objective anytime algorithms that find at each
+  iteration a solution to a bi-objective problem.
+
+  [Github](https://github.com/adbjesus/apm),
+  [Zenodo](https://doi.org/10.5281/zenodo.6856094)
+
+### moco\_abm
+
+  Rust library and binary to compute the ideal anytime behavior
+  theoretical model for bi-objective anytime algorithms that collect
+  an efficient solution at each iteration.
+
+  [Github](https://github.com/adbjesus/moco_abm),
+  [Zenodo](https://doi.org/10.5281/zenodo.2551046)
diff --git a/content/teaching/index.md b/content/teaching/index.md
new file mode 100644
index 0000000..1a98c38
--- /dev/null
+++ b/content/teaching/index.md
@@ -0,0 +1,31 @@
++++
+title = "Teaching"
++++
+
+### MSc
+
+- Experimental Methods in Computer Science
+  - [2022-2023](https://apps.uc.pt/courses/EN/unit/88863/20328/2022-2023)
+  - [2021-2022](https://apps.uc.pt/courses/EN/unit/88863/20328/2021-2022)
+  - [2020-2021](https://apps.uc.pt/courses/EN/unit/88863/20328/2020-2021)
+
+### BSc
+
+- Algorithmic Strategies (previously Advanced Programming Laboratory)
+  - [2021-2022](https://apps.uc.pt/courses/EN/unit/89047/20442/2021-2022)
+  - [2020-2021](https://apps.uc.pt/courses/EN/unit/89047/20442/2020-2021)
+  - [2017-2018](https://apps.uc.pt/courses/EN/unit/9865/669/2017-2018)
+- Compilers
+  - [2022-2023](https://apps.uc.pt/courses/EN/unit/9863/669/2022-2023)
+  - [2021-2022](https://apps.uc.pt/courses/EN/unit/9863/669/2021-2022)
+  - [2016-2017](https://apps.uc.pt/courses/EN/unit/9863/669/2016-2017)
+- Data Structures and Algorithms
+  - [2020-2021](https://apps.uc.pt/courses/EN/unit/9854/20442/2020-2021)
+- Introduction to Procedural Programming
+  - [2021-2022](https://apps.uc.pt/courses/EN/unit/9843/20442/2021-2022)
+  - [2020-2021](https://apps.uc.pt/courses/EN/unit/9843/20442/2020-2021)
+
+### Other
+
+- Introduction to Programming in Java
+  - [2013-2014](https://apps.uc.pt/courses/EN/unit/78102/14301/2013-2014)