Building research tools in public, one writing problem at a time.

What We’re Working On in StrataRead: A Smarter Library for Reading, Extracting, and Returning to Sources

StrataRead is growing from a focused PDF reader into a more complete reading library for research work. The goal is still intentionally narrow: help you read PDFs, capture the useful parts, and move those notes into the places where writing and synthesis happen.

The newest round of work is about making that loop feel sturdier. A source should be easy to import, describe, tag, search, annotate, export, and reopen later without having to remember where a PDF lives or which app last touched it.

A Real Research Library

The library view is getting more of the controls a working researcher needs once the PDF pile grows. StrataRead now has the foundations for sorting by date added, title, first author, year, and reading activity, along with filters for projects, tags, and read status.

That matters because reading is rarely linear. Sometimes you need the newest article, sometimes the unread items for a project, and sometimes every PDF tagged with a method, place, or concept. The library is being shaped around those practical retrieval moments.

Projects, Tags, and Batch Work

I am also adding better batch actions. Selected records can be assigned to a project, tagged together, exported, opened in another reader, or deleted as a group. On iPad, this pairs with edit-mode selection so the library feels less like a static list and more like a workspace.

Metadata That Starts With the PDF

StrataRead is also becoming smarter about bibliographic metadata. On import, it can look for a DOI in PDF metadata and the first pages of the document, then use Crossref to fill blank fields without overwriting deliberate edits.

The metadata model is expanding beyond journal articles too. Books, book chapters, and theses need different fields, and StrataRead is being adjusted so those sources can sit beside journal articles without being forced into the wrong shape.

Search From the Inspector

Search is moving into the inspector so it can live beside the metadata and extracts. You can search inside the active PDF, see result counts, jump forward or backward, and keep the source context visible while you work.

This is part of a larger shift: the inspector is becoming the command center for a source. It holds metadata, citation output, project and tag fields, freeform notes, search controls, and extracted annotations in one place.

Cleaner Extracts and Markdown Export

The extraction workflow is getting sharper. Highlights, underlines, strikeouts, and text notes can become structured extracts, with page anchors, annotation type, color information, and a path back to the source location in the PDF.

Those extracts can be copied or exported as Markdown with a citation, document notes, project and tag context, and a StrataRead deep link. The point is to make annotation portable: useful in StrataWrite, useful in Obsidian, and still connected to the original PDF.

Mac, iPad, and Private Sync

The interface work continues on both Mac and iPad. The app is being shaped around a three-column reading layout, a collapsible inspector, better iPad column behavior, and cleaner import/export flows. Underneath that, metadata syncs through CloudKit while PDFs live in the StrataRead iCloud Drive library.

The direction is simple: StrataRead should let a source move from PDF to extract to note without losing its citation, location, or context. Reading should leave useful traces, and those traces should be ready for writing.

What We’re Working On: Faster Search, Better iPad Workflows, and a More Native Writing Surface

StrataWrite has always been built around a simple idea: research writing is not just typing. It is moving between notes, sources, categories, drafts, questions, and the half-formed connections that eventually become an argument. The next round of work is focused on making those movements feel faster, calmer, and more native on both Mac and iPad.

A lot of the current work is not a single flashy feature. It is the kind of polish that makes the app feel more trustworthy during long writing sessions: better state updates after edits, clearer controls, fewer dead moments while search warms up, and a cleaner interface for moving across the research library.

A More Capable iPad Library

The iPad version is getting special attention. The research library sidebar is becoming more compact and more touch-friendly, with a cleaner workspace switcher for moving between the Library, Manuscripts, and Assets areas.

Selection mode is also being refined so batch actions feel less awkward on iPad. The goal is to make filtering, sorting, selecting, and acting on notes feel like an intentional iPad workflow, not a Mac interface squeezed onto a smaller surface.

Search That Keeps Up With Writing

I am also tightening the note search index. When a note changes, StrataWrite now does a better job of recognizing what actually needs to be updated and refreshing the related search data, summaries, and evidence context.

This matters because search is not just a utility feature in StrataWrite. It is part of the writing process. If search lags behind your notes, the library stops feeling alive. The goal is for recent edits, new notes, and related terms to become available quickly enough that you can keep thinking instead of managing the database.

The New Evidence Sheet

One of the bigger pieces growing out of this work is a new evidence sheet. When you search the library, StrataWrite can now prepare focused evidence passages from matching notes instead of leaving you with only a list of note titles.

The sheet is designed for the moment when a search becomes a research question. It can surface passages by mode, including general passages, key sources, methods, definitions, findings, and comparison points. It also adds section and signal filters, related terms, hit counts, source labels, copy actions, and links back into the original note.

I am also experimenting with an “Answer from Evidence” flow that synthesizes only from the retrieved passages and cites the sources it used. The intent is not to make the app write for you, but to make it easier to see what your own library can actually support before you start drafting a claim.

Markdown Actions Where You Need Them

On iPad, selected text is getting quicker Markdown actions directly in the edit menu. Bold, italic, highlight, and reader-note formatting can be applied without leaving the text selection flow. It is a small detail, but small details matter when you are shaping notes from source material all day.

Research Assets and DOI Refreshes

The Research Assets area is also being tuned. Controls for refreshing source DOIs and creating new assets are being renamed and clarified, with better accessibility hints and button labels. This is part of a larger effort to make sources, figures, tables, and research materials feel like first-class parts of the writing system.

A Calmer Dark Interface

Finally, the visual system is getting quieter. Dark mode surfaces are being deepened and card boundaries refined so the writing area feels less gray and more deliberate. The point is not decoration; it is reducing friction around long reading and writing sessions.

The common thread across all of this work is momentum. StrataWrite should make it easier to stay inside the argument: find the note, mark the passage, link the idea, draft the section, and keep moving.

I’ll share more as these changes settle, especially as the iPad workflow and research asset library continue to mature.

Introducing StrataRead

Over the past year, StrataWrite has grown from a focused writing experiment into the core of a broader research workflow. Today, I’m introducing a new companion app: StrataRead.

Together, these apps form StrataSuite, a set of research-first tools designed to support the full lifecycle of academic work: reading, annotation, synthesis, and writing.

StrataRead: Reading and Annotation

StrataRead is a PDF-first reading app built around annotation. It assumes that your real thinking happens in notes and writing, in tools like StrataWrite or Obsidian.

Rather than acting as a reference manager, StrataRead focuses on keeping PDFs organized and annotations accessible, so insights can move naturally into your existing note-taking workflow.

• Read and annotate PDFs
• Organize reading libraries for active research
• Move insights into notes and writing systems

StrataSuite Going Forward

Each app in StrataSuite is intentionally narrow in scope:

• StrataRead helps you engage deeply with PDFs and annotations
• StrataWrite is where synthesis and writing happen

Both apps are Apple-native, avoid analytics and tracking, and keep your data on-device or in your private iCloud account.

More details and a dedicated page for StrataRead are now live on the site. I’ll continue sharing development notes and updates here as the suite evolves.

Building StrataWrite: From Procrastination to Productivity

As a hobby project, I’ve created a new note-taking and writing app called StrataWrite. It began as an experiment for the Mac, and I’m now extending it to the iPad as well. I am an assistant professor, archaeologist, and unabashed Mac nerd.

My Apple journey started back in the 1990s as an undergraduate when I stumbled upon a lonely lab of Macintosh Classics. Everyone else gravitated to the PC labs, but the Mac immediately clicked for me. It worked the way my brain worked, and from then on I was hooked. Through graduate school and into my professional career, Macs have been my constant research and writing companions.

I write a lot for my research, but like many academics I’m also guilty of procrastinating by exploring workflows. StrataWrite started as another one of those experiments, perhaps even a procrastination crutch, but it has now grown into a tool I plan to use for real research and manuscripts.

Influences and Inspirations

I’ve used and loved apps like Ulysses for its minimalist interface, Scrivener for its power, and more recently Obsidian, Roam, and Craft. Obsidian fascinates me but never quite fits my process. The linking and Zettelkasten approach is brilliant for some, but I’m more of a structure-first thinker. For me, fast search and minimal structure beats elaborate organizing systems.

My Writing Process

My research writing begins with constant reading of PDFs: journal articles, chapters, and books. I highlight and annotate extensively. For citation management, I use Bookends by Sonny Software. It’s indie, Mac-first, and offers something I love: the ability to extract highlights with deep links back into the PDF. These links now integrate beautifully with StrataWrite.

Writing a research paper is always about structure: a central research question, supporting data, methodology, results, and contextual discussion. That structure is what organizes my notes. My students hear me say this often: without a research question, the paper collapses. StrataWrite reflects that same philosophy.

Why StrataWrite?

The name is inspired by archaeology. Strata are the layers of sediment and soil that accumulate over time, preserving artifacts of past lives. Similarly, StrataWrite layers notes, sources, and structures into something coherent. It also echoes ideas from practice theory and even assembly theory in physics.

How StrataWrite Works

At its core, StrataWrite is powered by plain text notes:

• Notes are searchable through Apple’s Core Spotlight.
• They can be filtered by categories: Document, Source, Note, and Journal.
• Search results are weighted by relevance, showing previews of context.

From there:

• Notes can be copied or exported as plain text files, individually or in bulk.
• Markdown preview makes links and formatting functional.
• Wiki-style links create connections between notes, supported by a Links Panel for navigation.

I’ve also experimented with on-device AI features using Apple’s new foundation models: summarization, keyword extraction, and question-answering for short notes. These are still limited by context size, but the promise of private, on-device models that can query all notes is on the horizon.

The interface also supports collapsing panels for a distraction-free writing mode. And everything syncs across devices using CloudKit.

The Manuscripts View

Beyond notes, StrataWrite now includes a dedicated Manuscripts view. This is a separate window designed specifically for long-form writing:

• Word goal tracking helps writers pace progress over time.
• A basic outlining tool structures your draft in sections.
• By keeping manuscripts separate from notes, the app creates a focused environment for drafting research papers or long essays.

Future Plans

StrataWrite is still evolving, but here is what is next:

• A Spreadsheet view for writers who prefer organizing information in tables.