:orphan:

.. include:: /_templates/include-file/page-prefix.rst


****************************************************************************************************
LLog: ResearchCity Key Papers Exhibit Pages — 2026m04d14
****************************************************************************************************

*Append-only audit trail for Prompt B: creating 19 exhibit pages for published scientific papers.*

| **VVN:** ``dv_ClaOp46_ExhB_2026m04d14``
| **Session:** 2026m04d14 -- 2026m04d15 (overnight build)
| **Model:** Claude Opus 4.6 (1M context)
| **Prompt file:** ``source/good-news-pack/vv/mmv3/llog/prompt-B_2026m04d14_researchcity-key-papers.rst``


Prompt (verbatim)
==================

.. container:: verbatim-prompt

   Read and execute prompt-B_2026m04d14_researchcity-key-papers.rst


Step 1: Context Reading
=========================

Read the following files as specified in the prompt:

1. ``.claude/CLAUDE.md`` — already loaded via system context
2. ``procedure-for-exhibit-page-generation.rst`` — full template and conventions
3. ``supporting-doc/sd1/index.rst`` — quality reference (SD1 Nuclear Winter exhibit)
4. ``mmv3/index.rst`` — master gateway for toctree registration
5. ``mmv3/collection-overview.rst`` — for status update


Step 2: PDF Reading
=====================

All 19 PDFs read successfully. Strategy:

- **Key papers** (6 papers flagged in prompt): read first 10 pages each
- **Remaining papers** (13 papers): read first 5 pages each
- Bibliographic data extracted from PDF content + filenames

.. list-table:: Papers processed
   :widths: 5 25 20 8 10
   :header-rows: 1

   * - #
     - Short title
     - Journal/Venue
     - Pages
     - PDF size
   * - 1
     - Loewe 1991 — Jugend Forscht
     - Jugend Forscht competition
     - 15
     - 16 MB
   * - 2
     - Loewe 2002 — Dissertation
     - TU München (PhD)
     - 444
     - 11 MB
   * - 3
     - Loewe 2002 — Global Computing
     - Briefings in Bioinformatics
     - 12
     - 128 KB
   * - 4
     - Loewe, Textor, Scherer 2003
     - **Science** 302: 1558--1560
     - 17
     - 900 KB
   * - 5
     - Loewe & Charlesworth 2006 DME
     - Biology Letters 2: 426--430
     - 6
     - 180 KB
   * - 6
     - Loewe 2006 Muller's Ratchet
     - Genetic Research 87: 133--159
     - 27
     - 1.7 MB
   * - 7
     - Loewe & Charlesworth 2007
     - Genetics 175: 1381--1393
     - 13
     - 600 KB
   * - 8
     - Loewe 2007 Evolution@home
     - Software: Practice & Experience
     - 30
     - 428 KB
   * - 9
     - Loewe & Hillston 2008
     - LNBI 5307: 156--175
     - 20
     - 2.0 MB
   * - 10
     - Loewe 2009 EvoSysBio
     - BMC Systems Biology 3:27
     - 34
     - 780 KB
   * - 11
     - Loewe, Moodie, Hillston 2009
     - EPTCS 6: 93--107
     - 15
     - 1.8 MB
   * - 12
     - Loewe, Moodie, Hillston 2009
     - Edinburgh Tech Report
     - 29
     - 4.8 MB
   * - 13
     - Loewe & Hill 2010
     - Phil Trans R Soc B 365
     - 15
     - 228 KB
   * - 14
     - Loewe 2012 EvoSysBio
     - Adv Exp Med Biol 751
     - 12
     - 244 KB
   * - 15
     - Ehlert & Loewe 2014
     - J Chem Phys 141: 204109
     - 20
     - 1.5 MB
   * - 16
     - James et al. 2014
     - XSEDE14 Workshop Report
     - 16
     - 492 KB
   * - 17
     - Loewe 2016 EvoSysBio Enc.
     - Enc Evol Biol 4: 297--318
     - 22
     - 2.2 MB
   * - 18
     - Loewe et al. 2017 Evolvix
     - Ann NYAS 1387: 124--144
     - 95
     - 2.7 MB
   * - 19
     - McLoone et al. 2018
     - Complexity 2018: 9836150
     - 14
     - 2.1 MB


Step 3: Exhibit Page Creation
===============================

**19 individual exhibit pages created**, each following the SD1 template:

- meta block, page-prefix include, short navbar title
- Full RST title with adequate overlines
- Download admonition (:class: note) with PDF link, size, pages, license, filename, WebP link
- Full-width WebP preview image
- AI overview (Abstract, Broader Significance, Who This Document Is For,
  Key Concepts at a Glance, Document Information, Related Documents)
- Footer (content-vvn, tidal-gradient, Notes dropdown, CTA, FF dropdown)

**Files created** (all in ``dusty-deep-data/loewe-researchcity-key-papers/``):

1. ``loewe-1991-jugend-forscht.rst``
2. ``loewe-2002-diss.rst``
3. ``loewe-2002-global-computing.rst``
4. ``loewe-textor-scherer-2003.rst``
5. ``loewe-charlesworth-2006-dme.rst``
6. ``loewe-2006-mullers-ratchet.rst``
7. ``loewe-charlesworth-2007.rst``
8. ``loewe-2007-evolution-at-home.rst``
9. ``loewe-hillston-2008.rst``
10. ``loewe-2009-evosysbio-framework.rst``
11. ``loewe-moodie-hillston-2009-eptcs.rst``
12. ``loewe-moodie-hillston-2009-techreport.rst``
13. ``loewe-hill-2010.rst``
14. ``loewe-2012-evosysbio-landscapes.rst``
15. ``ehlert-loewe-2014.rst``
16. ``james-2014-reproducibility.rst``
17. ``loewe-2016-systems-evosysbio.rst``
18. ``loewe-et-al-2017-evolvix.rst``
19. ``mcloone-et-al-2018.rst``


Step 4: Structural Updates
============================

1. **Created** ``dusty-deep-data/loewe-researchcity-key-papers/index.rst`` —
   subfolder index listing all 19 papers chronologically with highlights section.

2. **Created** ``dusty-deep-data/index.rst`` — parent folder index covering
   all three dusty-deep-data subfolders (key-papers done; about-me-science
   and about-me-spirituality noted as pending).

3. **Updated** ``mmv3/index.rst`` — added new toctree group "Background & Evidence"
   pointing to ``dusty-deep-data/index``.

4. **Updated** ``collection-overview.rst`` — changed Dusty Deep Data status from
   "pending" to "**key papers done** (19 exhibit pages, 2026m04d14); about-me pending".


Step 5: Build Check
=====================

``make clean && make dev`` run. Results:

- **0 new warnings** from our 19 exhibit pages or 2 index files
- 3 title overline warnings fixed during session (loewe-2007, loewe-charlesworth-2006, loewe-charlesworth-2007)
- Pre-existing warnings in other files remain (fishfus job positions, b11 checkmark refs, b15 structural deadlock) — not related to this session


Context Budget Notes
======================

- All 19 PDFs read successfully within session context
- First 6 key papers: 10 pages each (~60 pages total)
- Remaining 13 papers: 5 pages each (~65 pages total)
- Total PDF pages read: ~125 pages
- 19 exhibit pages + 2 index files written via parallel agent delegation
- 3 of 4 agent batches hit rate limits but completed their file writes before the limit
- No content was lost due to rate limits


Concluding Summary and Recommendations
=========================================

**Completed:** All 21 files created (19 exhibit pages + 2 index files),
structural updates applied, build tested clean.

**Remaining for Dusty Deep Data folder:**

- ``loewe-about-me-science/`` — 5 PDFs, exhibit pages pending
- ``loewe-about-me-spirituality/`` — 2 PDFs, exhibit pages pending

**Quality observations:**

- The 1991 Jugend Forscht paper is entirely in German — the abstract was
  translated for the exhibit page. Human review recommended.
- The 2002 dissertation abstract is bilingual (German Zusammenfassung + English Abstract);
  the English version was used.
- The James 2014 XSEDE report is a multi-author workshop report, not a single-author paper.
  LLoL was a participant, not a lead author. This is noted in the exhibit page.
- DOIs were extracted from PDFs where visible. Some older papers (1991, 2002 review)
  did not have DOIs visible in the PDF.

**Recommendation:** Review the 19 exhibit pages for accuracy of bibliographic details
and broader significance assessments. The abstracts are faithful to the PDF content
but the "Broader Significance" sections reflect Claude's assessment of how each paper
connects to the LLoL project.