CRESCYNT Toolbox: Workflows as Collaboration Space and Workbench Blueprint

puzzle-juggling_pixabayScientists need better ways to analyze and integrate their data and collaborate with other scientists; new computing technologies and tools can help with this. However, it’s difficult to overcome the challenge of disparate perspectives and the absence of a common vocabulary: this is true of multidisciplinary science teams, and true when scientists try to talk with computer scientists. Workflows, as a way to help design and implement a workbench, are needed both as a collaboration space and a blueprint for implementation.

Take a look at a recent presentation to the EarthCube science committee (video) or an earlier presentation offered at ASLO 2017 (slides and voice) to see a flexible and low-tech way to simultaneously (1) facilitate necessary sci-tech interactions for your own lab and (2) begin to sketch out a blueprint for work that needs to be done. Subsequent technical implementation is possible with new tools including Common Workflow Language (CWL) as a set of specifications, Dockers as modular and sharable containers for either fully developed tools or small pieces of code, and Nextflow as an efficient and highly scalable definitive software language to make the computational work happen. Look for a post in the near future by Mahdi Belcaid to describe the technical implementation of these workflows.

OPPORTUNITY! We will be hosting one or two in-person skills training workshops in the coming months, with your expenses covered by our NSF EarthCube CRESCYNT grant, focused particularly on training early career professionals, and will work through some challenging coral reef use cases and their cyberinfrastructure needs. We collected some great use cases at ICRS, but would like additional cases to consider, so we invite you to describe your own research challenges through this google form. Please contact us for more on this, or other issues. Thanks!

CRESCYNT Toolbox: Workflows as Collaboration Space and Workbench Blueprint

CRESCYNT Toolbox: Data Repositories – Estate Planning for your Data

“Hypotheses come and go but data remain.”    – Ramon y Cajal

Taking care of our data for the long term is not just good practice, allowing us to share our data, defend our work, reassess conclusions, collaborate with colleagues, and examine broader scales of space and time – it’s also estate planning for our data, and a primary way of communicating with future scientists and managers.


Here are some great options for long-term data storage, highlighting repositories friendly to coral reef science.

First, there are some important repository networks useful for coral reef data – these can unify standards and offer collective search portals: we like DataONE (members here) and bioCaddie (members here).

KNB – the Knowledge Network for Biocomplexity offers open and private data uploads; ecological orientation. DataONE network.

NOAA CoRIS: Coral Reef Information System – often free to use and can accept coral reef related data beyond NOAA’s own data; contact them first.

BCO-DMO – Biological and Chemical Oceanography Data Management Office – if you have an NSF grant that requires data storage here, you’re fortunate. Good data management guidelines and metadata templates, excellent support staff. Now a DataONE member.

Dataverse – supported by Harvard endowments. There are multiple organizational dataverses – the Harvard Dataverse is free to use. bioCaddie member.

Zenodo – free to use, supported by the European Commission (this is a small slice of CERN’s enormous repository for the Large Hadron Collider). Assigns dois. We invite you to include the “Coral Reef” community when you upload. bioCaddie member.

NCBI – the National Center for Biotechnology Information is very broadly accepted for ‘omics data of all types. A bioCaddie member.

DataCite – not a repository, but if you upload a dataset at a repository that does not assign its own doi’s, you can get one at DataCite and include it when publishing your datasets.

We’ve not listed more costly repositories such as Dryad (focused on journal requirements) or repositories restricted to institutions. What about other storage options such as GitHub, Amazon Web Services, websites? Those have important uses, but are not curated repositories with long-term funding streams, so are not the best data legacy options.

eggs-stacked-imagesMost of these repositories allow either private (closed) or public (open) access, or later conversion to open access. Some have API’s for automated access within workflows. These are repositories we really like for storing and accessing coral reef work. Share your favorite long-term data repository – or experiences with any of the repositories listed here – in the comments.

CRESCYNT Toolbox: Data Repositories – Estate Planning for your Data

CoralNet: deploying deep learning in the shallow seas – by Oscar Beijbom


Having dedicated my PhD to automating the annotation of coral reef survey images, I have seen my fair share of surveys and talked to my fair share of coral ecologists. In these conversations, I always heard the same story: collecting survey images is quick, fun and exciting. Annotating them is, on the other hand, slow, boring, and excruciating.

When I started CoralNet ( back in 2012 the main goal was to make the manual annotation work less tedious by deploying automated annotators alongside human experts. These automated annotators were trained on previously annotated data using what was then the state-of-the-art in computer vision and machine learning. Experiments indicated that around 50% of the annotation work could be done automatically without sacrificing the quality of the ecological indicators (Beijbom et al. PLoS ONE 2015).

The Alpha version of CoralNet was thus created and started gaining popularity across the community. I think this was partly due to the promise of reduced annotation burden, but also because it offered a convenient online system for keeping track of and managing the annotation work. By the time we started working on the Beta release this summer, the Alpha site had over 300,000 images with over 5 million point annotations – all provided by the global coral community.

There was, however, a second purpose of creating CoralNet Alpha. Even back in 2012 the machine learning methods of the day were data-hungry. Basically, the more data you have, the better the algorithms will perform. Therefore, the second purpose of creating CoralNet was quite simply to let the data come to me rather than me chasing people down to get my hands on their data.

At the same time the CoralNet Alpha site was starting to buckle under increased usage. Long queues started to build up in the computer vision backend as power-users such as NOAA CREP and Catlin Seaview Survey uploaded tens of thousands of images to the site for analysis assistance. Time was ripe for an update.

As it turned out the timing was fortunate. A revolution has happened in the last few years, with the development of so-called deep convolutional neural networks. These immensely powerful, and large nets are capable of learning from vast databases to achieve vastly superior performance compared to methods from the previous generation.

During my postdoc at UC Berkeley last year, I researched ways to adapt this new technology to the coral reef image annotation task in the development of CoralNet Beta. Leaning on the vast database accumulated in CoralNet Alpha, I tuned a net with 14 hidden layers  and 150 million parameters to recognize over 1,000 types of coral substrates. The results, which are in preparation for publication, indicate that the annotation work can be automated to between 80% and 100% depending on the survey. Remarkably: in some situations, the classifier is more consistent with the human annotators than those annotators are with themselves. Indeed, we show that the combination of confident machine predictions with human annotations beat both the human and the machine alone!

Using funding from NOAA CREP and CRCP, I worked together with UCSD alumnus Stephen Chan to develop CoralNet Beta: a major update which includes migration of all hardware to Amazon Web Services, and a brand new, highly parallelizable, computer vision backend. Using the new computer vision backend the 350,000 images on the site were re-annotated in one week! Software updates include improved search, import, export and visualization tools.

With the new release in place we are happy to welcome new users to the site; the more data the merrier!


– Many thanks to Oscar Beijbom for this guest posting as well as significant technological contributions to the analysis and understanding of coral reefs. You can find Dr. Beijbom on GitHub, or see more of his projects and publications here. You can also find a series of video tutorials on using CoralNet (featuring the original Alpha interface) on CoralNet’s vimeo channel, and technical details about the new Beta version in the release notes.

CoralNet: deploying deep learning in the shallow seas – by Oscar Beijbom

CRESCYNT Toolbox – Disaster Planning and Recovery

With computers, the question is not whether they will fail, but when.

tl;dr – It’s very practical to have cloud storage backup in addition to still-useful external hard drive backup routines. Here are some secure cloud alternatives.

itcrowd_giphyPersonal note. I’ve had hard drive failures due to lightning strike; simultaneous death of mirrored hard drives within a RAID; drenching from an upper floor emergency shower left flowing by a disgruntled chemistry student; and most recently, demise of my laptop by sudden immersion in salt water (don’t ask). By some intersection of luck and diligence, on each occasion recent backups were available for data recovery. In the most recent remake, it was a revelation how much work is now backed up via regular entry into the casual cloud.

This latest digital landing was mercifully soft (…cloudlike). Because of work portability, my recent sequential backup habit has been to a paid unshared Dropbox account; $10/mo is a bargain for peace of mind (beyond a certain size, restoration is not drag-and-drop). A surprising number of files these days are embedded in multiple team projects – much on Google Drive – so all of that was available, with revision history. Group conversations and files were on Slack and email. One auxiliary brain (iPhone)  was in a waterproof case with cloud backup, and another auxiliary brain (project/task tracking) was in a web app, KanbanFlow. Past years of long-term archives were already on external hard drives in two different cities. GitHub is an amazing place to develop, document, recover and share work in progress and products, but it is not a long-term curated data repository. For valuable datasets, the rule is to simplify formats, attach metadata, and update media periodically.

Thinking about your own locations for data storage and access? Check out this review of more secure alternatives to – and apps on top of – Dropbox. Some, like OwnCloud, can serve as both storage and linked access for platforms like Agave. A strength of some current analytical platforms is that they can access multiple data storage locations; for example, Open Science Framework can access Dropbox, Google Drive, GitHub, Box, figshare, and now Dataverse and Amazon Web Services as well.

A collaborator recently pointed out that the expense of any particular type of data storage is really the expense of its backup processes: frequency, automation, security, and combination of archiving media. Justifying the expense can come down to this question: What would it cost to replace these data? Some things are more priceless than others.

Disaster Planning and Recovery tools.  To go beyond data recovery in your planning, here’s an online guide for IT disaster recovery planning and cyberattacks. How much of a problem is this really? See Google’s real-time attack map (hit “play”). Better to plan than fear. You did update those default passwords on your devices, yes?

Feel free to share your own digital-disaster-recovery story in the comments.

CRESCYNT Toolbox – Disaster Planning and Recovery

CRESCYNT Toolbox: R Resources for Graphing and Visualization

In a previous post we offered some solid supportive resources for learning R – a healthy  dinner with lots of great vegetables. Here we offer a dessert cart of rich resources for data visualization and graphing. It’s a powerful motivation for using R.

First up is The New R Graph Gallery – extensive, useful, and actually new. “It contains more than 200 data visualizations categorized by type, along with the R code that created them. You can browse the gallery by types of chart (boxplots, maps, histograms, interactive charts, 3-D charts, etc), or search the chart descriptions. Once you’ve found a chart you like, you can admire it in the gallery (and interact with it, if possible), and also find the R code which you can adapt for your own use. Some entries even include mini-tutorials describing how the chart was made.” (Description by Revolutions.)

Sometimes we want (or need) plain vanilla – something clean and elegant rather than extravagant. Check out A Compendium of Clean Graphs in R, including code. Many examples are especially well-suited for the spartan challenge of conveying information in grayscale. The R Graph Catalog is a similar resource.

If you’re just getting started with R, take a look at the Painless Data Visualization section (p. 17 onward) in this downloadable Beginner’s Guide.

In R, ggplot2,  based on the Grammar of Graphics, is perhaps the single most popular R package for data visualization. The R Cookbook‘s section on Graphs using ggplot2 is a helpful precursor to the R Graphics Cookbook. DataCamp’s DataVis with ggplot2 has a free segment of intro lessons.

For more on visualization and other capabilities, check out this recommended list of useful R packages in the R Studio support blog – succinct and terrific.

If you’re already skilled in R and want a new challenge, an indirect method of harnessing some of the power of D3.js for interactive web visualizations is available through plotly for R. Here’s getting started with plotly and ggplot2, plotly and Shiny, and a gallery. The resources offer code and in some cases the chance to open a visualization and modify its data.

Have a favorite resource? Please share as a comment, or email us!

CRESCYNT Toolbox: R Resources for Graphing and Visualization

CRESCYNT Toolbox: Learning to love R more (or R is for reproducible)

caribbean_reef_shark_wikimediacommons_albertkokWe are driven to learn like sharks: constantly take in new flows, or die. In a recent workshop, when coral reef scientists were asked: “How many of you use R?” 60% raised a hand. To: “How many of you are comfortable with and love using R?” only about 15% kept a hand up.

Here’s where to go to learn to love R more.

rlogoYou likely already know of the R Project, free and open source software for statistical computing and graphics. You may already know of the reliability of the Comprehensive R Archive Network or CRAN repository, favored by many over other potential sources of community-generated code because of their metadata and testing requirements; it now hosts over 9,300 packages (sorted by date and name).

You may also know the elegance of RStudio, the excitement of putting your own interactive code online in RStudio’s Shiny, some great cheat sheets, the most popular R packages, and Stack Overflow as a great place to find answers to your R questions.

You may not know of the new R course finder, an online directory you can search and filter to find the best online R course for your next step (note there are often free versions or segments of even the pay courses listed). There are YouTube videos for R learning, like  twotorials (two-minute tutorials) and YaRrr! (because pirates) with book.

A very recent new book is getting rave reviews from both statistics and programming viewpoints: The Book of R by Tilman Davies (preview it here). The author writes:

“The Book of R …represents the introduction to the language that I wish I’d had when I began exploring R, combined with the first-year fundamentals of statistics as a discipline, implemented in R….   Try not to be afraid of R. It will do exactly what you tell it to – nothing more, nothing less. When something doesn’t work as expected or an error occurs, this literal behavior works in your favor….   Especially in your early stages of learning…try to use R for everything, even for very simple tasks or calculations you might usually do elsewhere. This will force your mind to switch to ‘R mode’ more often, and it’ll get you comfortable with the environment quickly.”

Because R is such a  stellar example of free and open source software with a very robust community (e.g., great stuff at r-bloggers), it’s a surprise how lucky we are that it IS open source, as heard in this interview with R founder Hadley Wickham on the podcast.

We’ll soon host a guest blogpost on some exploratory coral symbiont data analyses, visualizations, and comments generated in R Markdown, which is RStudio’s method for preserving code and output in one running web document. The work is beautiful and useful, and highlights the use of an electronic notebook as a way to capture and share data exploration, analysis and visualization, and to tell a data story. (A major advance to that software was announced this week in the form of R Notebook, which will ship within the next couple of months.)

Why is it worth learning to love R more?

R helps make sure your data work is reproducible (such an issue for science), repeatable (valuable for any processing you have to do periodically), and reusable (on other datasets or data versions, or by colleagues or your future self).

A couple of high-level languages, like R and Python, are becoming more popular each year, and are finding their way as general purpose tools into analytical platforms. These will serve as primary sources of flexibility in cyberinfrastructure platforms now available or under development. Our future selves thank us for the learning investment.

2016 Top 10 Tools for Analytics and Data Science - KD Nuggets Software Poll
“R, Python Duel As Top Analytics, Data Science software – KDnuggets 2016 Software Poll Results”  (click graph for article)

Update: speaking of interviews with R makers, here’s an October 2016 interview with JJ Allaire, the creator of RStudio, Shiny, and R Markdown. His advice for people new to R:

I would suggest that they get a copy of the R for Data Science book written by Hadley Wickham and Garrett Grolemund…. Also, when you have questions or run into problems don’t give up. There’s a lot of great activity around R on stackoverflow and other places and there’s an excellent chance you’re going to find the answers to your questions if you look carefully for them.
CRESCYNT Toolbox: Learning to love R more (or R is for reproducible)