Chore/manuscript update webserver

.gitignore

@@ -77,6 +77,8 @@ manuscript/**
 
 !manuscript/**/*.bst
 !manuscript/**/*.cls
+!manuscript/**/*.sty
 !manuscript/**/*.md
 !manuscript/**/
+!manuscript/graphical-abstract.html
 

CHANGELOG.md

@@ -1,5 +1,17 @@
 # Changelog
 
+## 1.16.1 — 2026-07-22
+
+### Fixes
+
+* **Disconnected nodes stay hidden across filter changes.** With "hide disconnected nodes" on, changing a filter could resurface a node that should have stayed hidden, and nodes that became disconnected by the change were never re-hidden. The dangling set is now recomputed against the current filtered view on every change.
+
+### Features
+
+* **Checkmark badge for single-value numeric filters.** Numeric properties with only one value (min === max) have no range to narrow, so they now show a read-only checkmark + value badge instead of an inert slider. The row's include/exclude checkbox still works.
+
+Also includes manuscript revisions (docs only, no app changes).
+
 ## 1.16.0 — 2026-07-22
 
 Saved graph files load unchanged. Stored bubble-set knob values keep applying, with two semantic shifts: padding and corridor width now scale with your configured node size (a value of 1 ≈ one node radius of margin) instead of absolute pixels, and any saved avoidance value above 0 now simply means "on".

manuscript/README.md

@@ -1,12 +1,32 @@
 # Graph Lens Lite — Publication
 
-Multi-venue LaTeX setup for the Graph Lens Lite paper. The body content lives in
-`shared/content.tex` and is rendered by two venue-specific drivers:
+LaTeX source for the Graph Lens Lite journal paper, targeting the OUP
+`oup-authoring-template` class (Nucleic Acids Research by default).
 
-| Directory  | Target venue           |
-|------------|------------------------|
-| `oxford/`  | Oxford Bioinformatics  |
-| `biorxiv/` | bioRxiv preprint       |
+The folder is flat: one driver (`main.tex`) plus the prose split into small
+`\input` files so each piece can be edited on its own.
+
+- `main.tex` — driver: preamble, frontmatter macros, `\input`s the body
+- `body.tex` — the body, Introduction through Conflict of interest
+- `abstract.tex` — abstract prose (no heading), fed to `\abstract{}`
+- `keywords.tex` — keyword list, fed to `\keywords{}`
+- `reference.bib` — bibliography database
+- `oup-plain.bst` — numbered citation style
+- `Fig/` — figures
+
+The body is in IMRaD order (Introduction → Materials and Methods → Results →
+Discussion); headings are unnumbered under the OUP class (`unnumsec`).
+
+## Author conventions
+
+Look for these markers when reviewing the draft:
+
+- `% AI-DRAFTED -- REVIEW` — prose drafted by an AI assistant during the
+  manuscript restructure. Treat as a starting point; revise in your own voice
+  before submission. Anything not marked is user-original prose preserved
+  verbatim from the prior draft.
+- `% TODO` — structural placeholder. The heading exists, the body is empty,
+  the comment block lists the angles to consider.
 
 ## Prerequisites
 
@@ -56,86 +76,49 @@ sudo tlmgr install natbib acronym preprint lineno enumitem lm
 
 ## Building
 
-Each flavor is compiled from its own directory. A full build requires
-`pdflatex` → `bibtex` → `pdflatex` → `pdflatex` (two extra passes resolve
-cross-references and citations).
-
-### Oxford Bioinformatics
-
 ```bash
-cd oxford/
 latexmk -pdf main
 ```
 
-Output: `oxford/main.pdf`
+Output: `main.pdf`
 
-### bioRxiv
+Uses the OUP `oup-authoring-template` class (`webpdf,contemporary,numbered`,
+numbered citations via `oup-plain.bst`). Set `\journaltitle` (and `\appnotes`)
+to the target venue at submission time.
+
+### Preprint / bioRxiv version
 
 ```bash
-cd biorxiv/
-latexmk -pdf main
+latexmk -pdf biorxiv
 ```
 
-Output: `biorxiv/main.pdf`
+Output: `biorxiv.pdf`
 
-### Build both at once
+`biorxiv.tex` is a second driver that reuses `body.tex`, `abstract.tex`, and
+`keywords.tex` verbatim under a plain `article` class — no OUP template
+needed. Drops the journal-specific frontmatter (title/DOI/vol/issue, the
+received/revised/accepted dates, two-column styling); keeps numbered
+citations (`natbib` + `unsrtnat`) and line numbers. Edits to the shared prose
+flow to both PDFs. `\ORCID{}` is a no-op here (bioRxiv collects ORCIDs in its
+submission form).
 
-From the manuscript directory:
+**The OUP class must be available.** It ships in recent TeX Live
+(`oup-authoring-template`); if `latexmk` reports the class missing, copy
+`oup-authoring-template.cls` and the `oup-*.bst` files from the OUP template
+(<https://www.overleaf.com/latex/templates/oup-general-template/ybpypwncdxyb>)
+into this directory, or build on Overleaf.
 
-```bash
-for dir in oxford biorxiv; do
-  (cd "$dir" && latexmk -pdf main)
-done
-```
+Note: the OUP class does not define the `description` environment — use
+`itemize` in the body.
 
 ### Clean auxiliary files
 
 ```bash
-cd oxford/   # or biorxiv/
 latexmk -C
 ```
 
-## Adding references
-
-`scripts/add_reference_to_manuscript.py` (in the repo root) fetches a PubMed
-citation by PMID and appends it to `shared/reference.bib`. It requires only
-Python 3 (no extra packages).
+## References
 
-```bash
-scripts/add_reference_to_manuscript.py <PMID>
-```
-
-The tool shows the generated BibTeX entry and asks for confirmation before
-writing. Duplicate cite keys are rejected automatically.
-
-## Repository structure
-
-```
-shared/
-  content.tex              Body sections shared across venues
-  abbreviations.tex        Acronym definitions
-  reference.bib            Bibliography database
-  Fig/                     Figures
-
-oxford/
-  main.tex                 OUP driver (structured abstract, journal metadata)
-  oup-authoring-template.cls
-
-biorxiv/
-  main.tex                 Preprint driver (article class, line numbers)
-
-../scripts/
-  add_reference_to_manuscript.py   Fetch PubMed citation → BibTeX (Python 3)
-```
-
-Edit `shared/content.tex` to change the paper body — both flavors pick up the
-changes. For small venue-specific differences inside the shared content, use the
-`\ifbiorxiv` flag:
-
-```latex
-\ifbiorxiv
-  Supplementary data are available at \url{...}
-\else
-  Supplementary data are available at \textit{Bioinformatics} online.
-\fi
-```
+Add entries to `reference.bib` (BibTeX). Citations render numbered in order of
+appearance via `oup-plain.bst`; NAR style shows the first three authors then
+"et al." — append `and others` to an author list to trigger it.

manuscript/abstract.tex

@@ -0,0 +1 @@
+Biological network visualization together with graph-based analyses are key techniques in systems biology and network medicine to detect patterns and generate hypotheses regarding disease pathobiology, drug target identification, biomarker prioritization, and digital drug discovery. Network representations provide an intuitive way to communicate and share research findings. We have developed Graph Lens Lite, a browser-based tool that combines rich visualization with a streamlined interface for exploring and sharing biological networks. It offers an expressive query language, topological network analysis, interactive filtering, visual grouping, customizable layouts, a data editor, fine-grained property-based styling, animated edge-flow visualization, community detection, and a context-aware locally powered AI assistant particularly suited for exploring molecular models of disease pathobiology or drug mechanism of action. We demonstrate its utility on a curated network model of autosomal dominant polycystic kidney disease. Graph Lens Lite is open source, with a live web version available at \url{https://delta4ai.github.io/GraphLensLite/}.