harisont · harisont · Jul 28, 2025 · Jul 28, 2025 · Jul 28, 2025 · Jul 28, 2025
diff --git a/README.md b/README.md
@@ -1,20 +1,18 @@
 A Search Tool for (parallel) Universal Dependencies treebanks that runs [in your browser](https://demo.spraakbanken.gu.se/stund).
 
-![STUnD GUI](img/replacement2.png)
+![STUnD GUI](docs/img/replacement2.png)
 
+While STUnD can also be used on single dependency treebanks, its most unique feature is that it allows running parallel queries on sentence-aligned UD treebanks by combining [UD-based subtree alignment](https://github.com/harisont/concept-alignment) with [UD tree pattern matching](https://github.com/harisont/deptreehs/blob/main/pattern_matching_and_replacement.md).
 
+## Learn more
 - [live demo](https://demo.spraakbanken.gu.se/stund)
-- [tutorial](tutorial.md)
-- [installation](installation.md)
-- [source code](https://github.com/harisont/STUnD)
-
-While STUnD can also be used on single dependency treebanks, its most unique feature is that it allows running parallel queries on sentence-aligned UD treebanks by combining [UD-based subtree alignment](https://github.com/harisont/concept-alignment) with [UD tree pattern matching](https://github.com/harisont/deptreehs/blob/main/pattern_matching_and_replacement.md).
+- [docs]([tutorial.md](https://harisont.github.io/STUnD/))
 
+## Citing
 STUnD is a Haskell+JavaScript web application built by Herbert Lange and Arianna Masciolini based on an initial prototype by Arianna Masciolini. 
 
-## Citing
 If you use this tool in your research, you are welcome to cite
 
-> [Arianna Masciolini and Márton A Tóth. _STUnD: ett Sökverktyg för Tvåspråkiga Universal Dependencies-trädbanker._ In Proceedings of the Huminfra Conference, pages 95–109, Gothenburg, Sweden, 2024](https://doi.org/10.3384/ecp205013) ([bibtex](stund.bib)).
+> [Arianna Masciolini and Márton A Tóth. _STUnD: ett Sökverktyg för Tvåspråkiga Universal Dependencies-trädbanker._ In Proceedings of the Huminfra Conference, pages 95–109, Gothenburg, Sweden, 2024](https://doi.org/10.3384/ecp205013) ([bibtex](docs/stund.bib)).
 
 A more extensive and up-to-date publication in English is currently in preparation.
diff --git a/_config.yaml → docs/_config.yaml b/_config.yaml → docs/_config.yaml
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 show_excerpts: false
 
-remote_theme: jekyll/minima
+remote_theme: "jekyll/minima@1e8a445"
 
 minima:
   skin: dark
   date_format: "%-d %B %Y"
   social_links:
     - { platform: github, user_url: https://github.com/harisont }
-    - { platform: stackoverflow, user_url: https://stackoverflow.com/users/7729724/harisont }
     - { platform: instagram, user_url: https://www.instagram.com/unottica/ }
     - { platform: youtube, user_url: https://www.youtube.com/c/ImparalHaskellemettilodaparte }
-    - { platform: rss, user_url: https://harisont.github.io/feed.xml}
 
 plugins:
   - jekyll-feed
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     <div class="footer-col-wrapper">
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-        <p class="feed-subscribe">
-          <a href="https://harisont.github.io/feed.xml">
-            <svg class="svg-icon white">
-              <use xlink:href="{{ 'assets/minima-social-icons.svg#rss' | relative_url }}"></use>
-            </svg><span>Subscribe to the blog</span>
-          </a>
-        </p>
       {%- if site.author %}
         <ul class="contact-list">
           {% if site.author.name -%}
@@ -28,10 +21,6 @@
       </div>
     </div>
 
-    <div class="social-links">
-      {%- include social.html -%}
-    </div>
-
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 </footer>
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@@ -0,0 +1,20 @@
+A Search Tool for (parallel) Universal Dependencies treebanks that runs [in your browser](https://demo.spraakbanken.gu.se/stund).
+
+![STUnD GUI](img/replacement2.png)
+
+
+- [live demo](https://demo.spraakbanken.gu.se/stund)
+- [tutorial](tutorial.md)
+- [installation](installation.md)
+- [source code](https://github.com/harisont/STUnD)
+
+While STUnD can also be used on single dependency treebanks, its most unique feature is that it allows running parallel queries on sentence-aligned UD treebanks by combining [UD-based subtree alignment](https://github.com/harisont/concept-alignment) with [UD tree pattern matching](https://github.com/harisont/deptreehs/blob/main/pattern_matching_and_replacement.md).
+
+STUnD is a Haskell+JavaScript web application built by Herbert Lange and Arianna Masciolini based on an initial prototype by Arianna Masciolini. 
+
+## Citing
+If you use this tool in your research, you are welcome to cite
+
+> [Arianna Masciolini and Márton A Tóth. _STUnD: ett Sökverktyg för Tvåspråkiga Universal Dependencies-trädbanker._ In Proceedings of the Huminfra Conference, pages 95–109, Gothenburg, Sweden, 2024](https://doi.org/10.3384/ecp205013) ([bibtex](stund.bib)).
+
+A more extensive and up-to-date publication in English is currently in preparation.
diff --git a/installation.md → docs/installation.md b/installation.md → docs/installation.md
@@ -3,13 +3,13 @@ title: Installation
 layout: base
 ---
 
-# Installation
+# Local installation
 
-To compile and run STUnD directly on your computer, you can use either [the Haskell Tool Stack](https://docs.haskellstack.org/en/stable/) or build and run it inside a [Docker](https://www.docker.com/) container.
+To compile and run STUnD on your computer, you can use either [the Haskell Tool Stack](https://docs.haskellstack.org/en/stable/) or build and run it inside a [Docker](https://www.docker.com/) container.
 
 In either case, start by downloading the [source code](https://github.com/harisont/STUnD).
 
-## Installation via Stack
+## Installing STUnD via Stack
 If you have Stack, run  
 
 ```
@@ -33,4 +33,9 @@ If you want to use Docker containers, the simplest way is to use `docker compose
 docker compose up stund-gui
 ```
 
-This will take a while for the first time because the image has to be built. Afterwards, running the container can be started directly with the same command.
+This will take a while for the first time because the image has to be built. Afterwards, running the container can be started directly with the same command.
+
+---
+
+For troubleshooting Windows installations, see [here](win.md).
+For details about deployment at SBX, see [here](deployment.md).
diff --git a/mstile-150x150.png → docs/mstile-150x150.png b/mstile-150x150.png → docs/mstile-150x150.png
diff --git a/pub.md → docs/pub.md b/pub.md → docs/pub.md
@@ -3,8 +3,8 @@ title: Publications
 layout: base
 ---
 
-# Publications using STUnD
+# Publications
 
-1. [Arianna Masciolini and Márton A Tóth. _STUnD: ett Sökverktyg för Tvåspråkiga Universal Dependencies-trädbanker._ In Proceedings of the Huminfra Conference, pages 95–109, Gothenburg, Sweden, 2024](https://doi.org/10.3384/ecp205013)
+1. [Arianna Masciolini and Márton A Tóth. _STUnD: ett Sökverktyg för Tvåspråkiga Universal Dependencies-trädbanker._ In Proceedings of the Huminfra Conference, pages 95–109, Gothenburg, Sweden, 2024](https://doi.org/10.3384/ecp205013) ([bibtex](stund.bib)): this paper describes STUnD's first prototype and exemplifies its usage through a small case study on a bilingual treebank
 
 A more extensive and up-to-date publication in English is currently in preparation.
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diff --git a/docs/tutorial.md b/docs/tutorial.md
@@ -0,0 +1,140 @@
+---
+title: Tutorial
+layout: base
+---
+
+# Getting started with STUnD
+
+## Specifying the input files
+![start screen](img/start.png)
+
+The "Browse..." buttons are used to specify one or two (parallel) input files, which have to be in either __strict [CoNNL-U format](https://universaldependencies.org/format.html)__ or __"horizontal" plain text__ (one sentence per line). 
+
+Plain text files are parsed with the [UDPipe 2 API](https://lindat.mff.cuni.cz/services/udpipe/api-reference.php), using the default model for the language they are written in.
+The language can be made explicit as a two-letter code followed by an underscore in the beginning of the name of the file (for example, an input file called `sv_rawtext.txt` would be assumed to be in Swedish). 
+If this is not the case, the language is automatically inferred.
+
+If you only specify the input file(s), leaving the other fields blank, clicking "Search" will run a default query that retrieves all sentences in the treebank(s):
+
+![null search](img/null_search.png)
+
+## Running a query
+Queries are specified in the first text input field:
+
+![query for presens perfekt](img/presens_perfekt.png)
+
+(note that double clicking on it will show the query history).
+
+### Monolingual queries
+The example query in the picture is
+
+```haskell
+TREE_ (FEATS_ "VerbForm=Sup") [AND [LEMMA "ha", FEATS_ "Tense=Pres"]]
+```
+
+This is a _simple_ or _monolingual_ query, looking for present perfect constructions in the Swedish treebank.
+It reads as
+
+> Look for (sub)trees (`TREE_`) where the root is a supinum (`(FEATS_ "VerbForm=Sup")`), one of whose direct dependents is the present of the verb "ha" (`AND [LEMMA "ha", FEATS_ "Tense=Pres"]`).
+
+Now only the subtrees matching the query (often full trees in this case) are highlighted in bold (cf. last row). 
+
+With some knowledge of Swedish, this particular query can be rewritten more concisely as
+
+```haskell
+TREE_ (FEATS_ "VerbForm=Sup") [FORM "har"]
+```
+
+It is then very easy to modify the query for other structurally similar tenses:
+
+- `TREE_ (FEATS_ "VerbForm=Sup") [FORM "hade"]` (pluperfect)
+- `TREE_ (FEATS_ "VerbForm=Sup") [FORM "ha"]` (perfect infinitive)
+
+Compared to the original "present perfect" query, these make it easier to see how queries work: first, the program tries to align the two treebanks to identify semantically equivalent subtrees; then the query is run on the left (Swedish) treebank  (T1) and matching subtrees are returned alongside their English counterpart (T2).
+
+__Unlike query matching, the alignment step is not guaranteed to find _all_ correspondences__: in the picture above, you can see that sometimes a match is found in the Swedish treebank but nothing is highlighted in the corresponding English sentence (cf. row 4). 
+Some other times, a correspondence is found but is incorrect. 
+These two outcomes can be caused both by annotation errors and limitations of the alignment algorithm, which relies on a set of syntax-based heuristics.
+
+Of course, monolingual queries can also be run on single treebanks:
+
+![monolingual query on single treebank](img/single.png)
+
+### Parallel queries
+Queries can also be _parallel_ or _bilingual_. For instance, we can use the following pattern to search for sentences where a Swedish present perfect corresponds to a passive present tense in English:
+
+```haskell
+TREE_ (FEATS_ "VerbForm={Sup->Part}") [AND [LEMMA "{ha->be}", FEATS_ "Tense=Pres"]]
+```
+
+This produces the following results:
+
+![bilingual query](img/bilingual_query.png)
+
+Note that the second hit here is a false positive, due to the fact that "are" in the clause "there are already..." is also a direct dependent of the main lexical verb "dropped".
+This is unfortunate, but difficult to avoid given how conjuncts are treated in UD.
+
+The basic query language ("UD patterns") is described [here](https://github.com/harisont/deptreehs/blob/main/docs/patterns.md), while its extended version for parallel (bilingual) queries (`{X -> Y}` syntax) is documented [here](https://github.com/harisont/L2-UD#l1-l2-patterns).
+
+## Refining the search results
+The second input field can be used to specify a _replacement rule_ to be applied to all matching subtrees in both languages.
+This can help highlight and manipulate the relevant parts of each query result them.
+
+Understanding replacement rules, which are described [alongside the basic query language](https://github.com/harisont/deptreehs/blob/main/docs/patterns.md), can be slightly more challenging.
+
+As a first example,
+
+```haskell
+PRUNE (UPOS "VERB") 0
+```
+
+decreases the depth of trees rooted in a verb to 0, eliminating all dependents:
+
+![drastic pruning](img/replacement1.png)
+
+The more complex pattern
+
+```haskell
+CHANGES [FILTER_SUBTREES TRUE (OR [DEPREL_ "aux", DEPREL_ "cop"]), PRUNE TRUE 1]
+```
+
+uses dependency labels to isolate verb constructions of maximum depth 1, thus producing, in conjunction with the first query, the following output:
+
+![replacement rule](img/replacement2.png)
+
+## CoNNL-U and tree mode
+So far, we have discussed how to use STUnD in plain text mode.
+Switching to CoNNL-U mode allows inspecting the CoNNL-U (sub)trees __corresponding to bold text in the default text mode__:
+
+![CoNNL-U mode](img/conllu.png)
+
+Tree mode renders them as SVG trees:
+
+![Tree mode](img/tree.png)
+
+## Saving the search results
+Query results can be saved as TSV, CoNNL-U and HTML-embedded SVG trees. 
+The output format depends on the mode in which STUnD is used: in the example above, for instance, results would be saved in SVG.
+
+Results obtained on parallel treebanks can be saved as two separate files, one per treebank, by clicking on "T1 file" and "T2 file" respectively, or as a single file by choosing "parallel file":
+
+- in text mode, the T1 and T2 files are horizontal text files, while the parallel file is TSV. This makes it easy to import search results in any spreadsheet program
+- in CoNNL-U mode, the output is always a new CoNLL-U treebank that can be used, for instance, as input for more refined queries in StUnD, or simply imported into [another CoNNL-U viewer](https://universaldependencies.org/conllu_viewer.html) for further inspection. In parallel files, sentences from the two input treebanks are interleaved
+- similarly, parallel files in tree mode alternate T1 with T2 trees
+
+## Other functionalities
+
+### Validation
+STUnD performs some basic (i.e. __less strict than the [official UD validator](github.com/UniversalDependencies/tools/blob/master/validate.py)__) validation of the input data, checking that all word lines contain 10 tab-separated fields, as well as that all token IDs, UPOS tags and DEPRELs are valid as per the [UD universal annotation guidelines](https://universaldependencies.org/guidelines.html).
+If your treebank contains one or more format errors, these are listed in the user interface:
+
+![format errors](img/format_error.png)
+
+### Diff mode
+Diff mode, activated by checking the "diff" box, helps you identify discrepancies between two similar treebanks. 
+This feature can be useful when exploring parallel (error-correction) learner treebanks, as well as when comparing alternative analyses of the same text, as in the following example:
+
+![format errors](img/diff_tree.png)
+
+### Manual editing
+On top of replacement patterns, which can be used to apply systematic changes to the input treebank(s), basic manual editing functionalities are available in CoNLL-U mode.
diff --git a/win.md → docs/win.md b/win.md → docs/win.md
@@ -1,4 +1,4 @@
-# Compiling on Windows
+# Known issues (Windows)
 It appears that `curl`, __but not `curllib`__, is installed by default on Windows10+. Therefore it is necessary to:
 
 1. Download and extract `curl` binaries for windows(https://curl.se/windows/)

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