Publication types - The Stacks docs

The Stacks aims to expand the definition of what is “publishable”, and enable rapid publishing of a variety of outputs from the scientific process. Its goal is to enable flexible and continuous publishing, with embedded metadata giving the reader information about what was published, why, and what it means.

Each publication is tagged with a Pub Type. Below is a brief summary of each, and examples for you to learn from.

Idea¶

A proposal or hypothesis you haven’t tested yet. Sharing it early invites collaborators and critique before you invest in the work.

Biology needs to become prospective

Since biological data are often non-independent, more data doesn't always mean more insight. We argue that a prospective approach is needed to uncover the deepest principles of life.

Defining actin: Combining sequence, structure, and functional analysis to propose useful boundaries

The process of deciding whether a candidate actin homolog represents a “true” actin is tricky. We propose clear and data-driven criteria to define actin that highlight the functional importance of this protein while accounting for phylogenetic diversity.

Open question¶

A question you’re stuck on, or one you think the field should answer. It asks readers for their experience, data, or suggestions.

How can we measure and communicate the impact of science?

How can we measure the true impact of science? We're seeking feedback on indicators of the utility and rigor of publications beyond traditional journal metrics. Your input will help shape the future of our publishing experiment.

How do we balance labor and yield in high-throughput protein expression?

We need to test hundreds of in silico protein variant designs in the lab. We have automated purification strategies, but expressing enough protein to purify is low-throughput and rate-limiting. Can we crank up expression without big, unwieldy culture flasks and intensive effort?

Observation¶

Something unexpected you noticed but haven’t fully explained. It puts a curious result on the record so others can build on it.

Chlamydomonas cpc1-1 mutant exhibits unexpected growth phenotypes

Comparative analysis of Chlamydomonas strains revealed that a cpc1-1 mutant has three unexpected growth phenotypes across different media types, suggesting possible genetic background contributions beyond characterized mutations.

Morphological transformation of Chlamydomonas smithii grown in Marine Broth medium

Marine Broth induces extreme morphological transformation in C. smithii: Cells shift from typical ellipsoid shape to amorphous forms with thin wisp-like appendages containing mitochondria, revealing unexpected cellular plasticity.

Method¶

A new or improved way to do something, described in enough detail to reuse. It helps others adopt your approach without reinventing it.

A method for computational discovery of viral structural mimics

Some parasites use mimics of host proteins to manipulate host pathways. We’ve developed a mimicry detection pipeline and benchmarked it using well-studied viral mimics. The pipeline successfully recovers known mimics and is ready for deployment at scale.

An experimental and computational workflow to characterize nematode motility behavior

We used straightforward microscopy and computational analyses to reproducibly characterize a nematode motility phenotype with interpretable features. This method should be scalable for high-throughput phenotypic screening.

Result¶

A finding from experiments or analysis, with the data behind it. It’s closest to a traditional paper, but can be smaller and faster to share.

Interpretable neural networks reveal global epistasis in yeast

We applied a mechanistic interpretability approach to neural networks trained on a large yeast genotype–phenotype dataset. This allowed us to uncover novel evidence of environmentally mediated global epistasis in these data.

A single bead improves fission yeast liquid culture growth

Growing S. pombe liquid cultures with a bead yields more homogeneous, denser, and faster-growing cultures, without cell sedimentation. We found that, with a bead included, we could grow cultures in larger volumes and narrower vessels without sacrificing cell quality.

Dataset¶

Data you collected or assembled, with enough context for others to reuse it. It makes your data findable and citable on its own.

Coherent Raman imaging of live, unfixed Saccharomyces cerevisiae and mutants aah1∆ and rad6∆

We acquired single-cell coherent Raman microscopy data (SRS and CARS) from wild-type budding yeast and two mutants. Our aim was to collect spatially resolved biochemical data on living yeast cells. We’re sharing the data and code for others to visualize and explore it!

Assembling and annotating an Asgard archaea and giant virus dataset of over 840,000 proteins

We assembled a comprehensive dataset of proteins from Asgard archaea and giant virus genome assemblies. This dataset lets us explore protein sequence and structure relationships more broadly across the tree of life to better understand protein structure and function.

Resource¶

A tool, software package, workflow, or other material that others can use directly. It explains what the resource does and how to use it.

A free, open-access library of high-quality organism illustrations for science communication

We create vector graphics of model organisms and emerging biological research organisms to enhance our publications. We’re sharing these editable graphics under a CC0 license for other scientists to use in figures, slides, teaching materials, or other outputs.

ProteinCartography: Comparing proteins with structure-based maps for interactive exploration

The ProteinCartography pipeline identifies proteins related to a query protein using sequence- and structure-based searches, compares all protein structures, and creates a navigable map that can be used to look at protein relationships and make hypotheses about function.

Negative data and informative failures¶

An experiment or approach that didn’t work, and what you learned from it. It saves others from repeating the same dead end.

Leave-one-batch-out cross-validation reveals strong batch effects in Raman spectroscopy of yeast cultures

We acquired spontaneous Raman spectra of several strains and species of yeast. We found that experimental batch effects dominate strain-level biological signals in our dataset, yielding misleadingly high classification accuracy under standard cross-validation.

Joint steering of protein generation across multiple target properties

Most guided-generation methods optimize one or two properties, but a usable protein has to clear several bars at once. We steered fluorescent protein generation with predictors of excitation and emission peaks and of brightness. Guided designs came closer than filtered ones.

Perspective¶

Your view on a field, an approach, or how science gets done. It starts conversations that don’t fit in a research report.

Closing the divide between analysis and publication: The notebook pub

We're experimenting with treating our computational notebooks as publications themselves. This approach reduces publication burden, encourages faster publishing, and builds in reproducibility. Scientists can publish with minimal extra effort.

Icebox is a science-sharing strategy designed to encourage risk-taking

Our "icebox" is where we share the projects that we've decided not to continue. We surveyed our company to understand resulting cultural shifts and how others are carrying our iced work forward.