Translational Research Workflow and Tools

At any given time, the 3D Lab has 3-5 students, RAs, and technologists working with a half a dozen collaborators across the hospital and Brown on multiple projects. I do very little actual science anymore; I mostly organize research projects. So I have become increasingly interested in academic productivity and organization tools.

The academic research workflow at the hospital is basically something like this:

  1. We meet with some clinical or academic collaborators, we discuss a project, write some notes, emails are exchanged, preliminary results are shared as things start to happen
  2. I start to organize our ideas and preliminary results into a narrative
  3. We decide that we are going to pursue some discrete project goal and figure out what we need to do to make it happen
  4. I have to pull everything together, often drawing on templates created in previous projects, to create one or more final, finished product(s)

Each of those phases have distinct goals for data organization. I would generalize each step of that process as follows:

Translational Research Notebook Goals by Stage

  1. I want to keep a record of what is happening
  2. I want to organize a record about what has happened
  3. I want to organize a record about what will/must happen
  4. I want to present/share/save a record

There is no "silver bullet" single application for organizing such a general workflow. I will comment on some of the different types of tools I have found helpful for each part. I italicized the tools I have been using recently. Also, we are primarily Mac-based, but we need to support clinician collaborators who are primarily Windows-based.

1. Tools for organizing now (note taking)

  • nvAlt, Notational Velocity, Simplenote, Textwrangler, Notepad, etc. are very fast, text only, no data attachments, nvAlt syncs through Simplenote's interface
  • Evernote, OneNote, Curio support rich media, but are proprietary, have no effective data liberation policy. I recently explicitly abandoned Evernote because I was concerned about data liberation.
  • Zotero for grabbing references and bibliographic info is open and extensible. I tried other ref managers, including Endnote, and didn't like them as much
  • Time tracking software

Important to me: simple, fast, open, searchable, cross-linkable, sync (always available)

2. Tools for organizing the past (creating a narrative)

  • Circus Ponies Notebook (CPN), OmniOutline, Scrivener, Tree for outlining
  • VoodooPad or other personal wiki's, but they seem somewhat difficult to organize to surprisingly uncollaborative
  • DevonThink is too cumbersome
  • Zotero for organizing reference collections
  • Aeon Timeline (I wish there were more tools for temporal organization out there)
  • Dropbox and the like for collaborative data sharing, I also have to run a DICOM server
  • Bitbucket, GitHub for code versioning

Important to me: multiple organization paradigms (hierarchy, linear, cross-links, columns), rich media support, annotatable, open

3. Tools for organizing the future (project planning)

  • Basecamp, Podio, Asana for collaborative todo's, updates, no data liberation
  • MS Project, Gantter, and the like for time management
  • MS Excel for budgets

Important to me: robust, collaborative, open

Tools for presenting narrative (rendering documents)

  • MS Word, OpenOffice, Acrobat for final formatting (doc, odf, and pdf are reasonable archival formats)
  • Visio, LucidCharts for diagramming
  • Marked for previewing Markdown rendering
  • Scrivener, Ulysses for organizing writing projects
  • Latex for technical writing (I've moved away from this b/c I don't like how cryptic it is)
  • Zotero for building bibliographies
  • The web (see my note on setting up a webserver)

Important to me: Easy to pull from different sources, separates creation from presentation, collaborative, versioning

Currently, I use a hodgepodge of things, some that seem best for the task at hand, others that seem like they will make it easier to accomplish something downstream. For example, I'm a fan of Multimarkdown because I can use the same markdown formatted blob of information in all parts of my workflow form the beginning up until the very end when you render it into its final rich text format. I use Basecamp and Bitbucket in part because they have an academic discount policy.

Ideally, I would like to use something that looks like circus ponies as an organizing metaphor across the workflow. I write quick notes in markdown. Drag a bunch of them into CPN, reorganize it into a narrative and create sections and relationships between the material, attach rich media, pdfs, other supporting documents, and use that as my default place to keep data at rest. I have a bookshelf of notebooks for different projects in different states and a few master notebooks that serve as indices (perhaps organized by year, by project domain, by collaborator...). Each notebook might have a todo list and a calendar and assignments of particular pages to particular people. Finally, when I need to generate a paper or a presentation, I can organize it as a tab in a project notebook and then export the structure, notes, references, etc. to Word or Powerpoint where I can tweak it into a final formatted product.