Cool online presentations with free software

It has been a while since I wrote a tutorial to Share The Wealth, so it’s about time I shared some practical (if basic) knowledge beyond reposting a link.

For years I have had a pet project in the backburner: I wanted to create presentations without the need of dedicated software, commercial (like PowerPoint or Keynote), or free (like LibreOffice or OpenOffice). That way I could avoid bringing my computer to a lecture, and not worry about what computer system would be available in the auditorium. As long as there is internet connectivity or a USB port, I can bring a URL and a USB as a backup, and it will work.

I also wanted some minimum functionality like:

  • Being able to print the presentation or export it into PDF
  • Keyboard controls (including overview)
  • Accesible from any device
  • Progress bar
  • Transitions and effects
  • Reproducible in any browser without the need of any plug-in or additional software
  • Presenter window with next slide, notes and countdown
  • All in a file format that is easy to use, like HTML or Markdown

Of course, your wishes shall be granted by the gods of Free Software. Behold the no-dependencies JavaScript Reveal.js.

But to make the presentation truly awesome, there were a few more things I needed to do, like incorporating it into my Git workflow (for branches, versions, and all those Git goodies) and hosting it.

Let me walk you through the process, so you can also be up and running with Presentation Awesomeness in no time:

First, create a new repository on GitHub or GitLab (if you don’t know what that is, you need to read other tutorials first). For this tutorial, I’ll use GitHub, although in the office we use Gitlab.

Give your presentation a name, like “MyPresentation”.

Clone it to your local machine. You can use the GUI application (I like the new Electron-based beta), or use the CLI (“Terminal” for Apple OSX users):

git clone git@github.com:yourusername/MyPresentation.git
[Obvious note: substitute “yourusername” for your user name]

Clone reveal.js onto your local machine. This time:
git clone git@github.com:hakimel/reveal.js.git

Go to the File System (“Finder” in OSX), locate your Git working directory (“Folder” in OSX), and move (or copy) the content of the directory “reveal.js” to the “MyPresentation” folder.

Modify the index.html file. This is where your presentation content and format goes. Take a look at the detailed tutorial here.

Once done, “push” the project to your Git. If using the CLI:
git push

Feel free to use Grunt for local dynamic serving. Some people even use generator-reveal, a Yeoman generator, to have each slide as an individual HTML or Markdown file.

If you are using GitHub, now, “automagically”, your slides are published at yourusername.github.io/MyPresentation

One more detail: if you want to access the slides themselves (for a hosted presentation) instead of the “repo” (repository of all the files you just “pushed”), you need to go to GitHub and enable “GitHub pages” in this particular repository. Just go to the repository index.html page in GitHub, and select the down-arrow menu icon on the upper right (nexto to “insights”) “settings>pages” and activate GitHub pages for that repo.

Additionally, there are many plugins you can use with reveal.js, like kreator. Enjoy!

Visiting the London Design Museum

Yesterday I visited the Design Museum (“The world’s leading museum devoted to contemporary design in every form from architecture and fashion to graphics, product and industrial design”) in its spectacular new location on High Street Kensington (London), with my son.

The #newdesignmuseum opened its doors in its new location only 5 days ago. The building and renovation are great, and in a nice location: on the edge of Holland Park, with the added bonus of being near the Kyoto Garden, Muji, and not far from the Serpentine Gallery.

I was expecting more from the shop(s) and I felt the exhibitions lacked a more daring curating, and more compelling communication. Although the loose “Designer, Maker, User” theme was not bad, they could have definitely dug more into the concept.

Additionally, it felt the collection was not comprehensive enough, with an overwhelming majority of consumer electronic devices, and not enough from other disciplines like fashion, architecture, or even manufacturing.

All in all, a nice evening in a nice museum, but plenty of room for improvement.

Award and Exponential Medicine Conference San Diego day 2

Sunday, October 9th, was day two at Exponential Medicine Conference in San Diego.

Some of the highlights were:

From ‘Omics to Action

  • Moira Gunn, PhD Host, NPR’s Biotech Nation
  • Larry Smarr, PhD Professor, UCSD and Director, Calit2
  • George Poste, DVM PhD FRS Chief Scientist, Complex Adaptive Systems Initiative- Arizona State University

Mobile, Connected, Digital Health

  • David Albert, MD Founder, AliveCor
  • Stanley Shaw, MD PhD Co-Director, MGH Center for Assessment Technology & Continuous Health
  • Bakul Patel, MBA Associate Director of Digital Health, Food and Drug Administration/Center for Devices and Radiological Health
  • Ulrik Wisløff Professor: Faculty of Medicine, Norwegian University of Science and Technology

Innovating at Scale: John Mattison, MD CMIO and Assistant Medical Director, Kaiser Permanente

Connecting the Dots: Mark Hyman, MD Chairman, Institute for Functional Medicine

Future of Intervention

  • Catherine Mohr, MD Vice President of Strategy, Intuitive Surgical
  • Tippi MacKenzie, MD Professor of Pediatric Surgery, UCSF
  • Amir Szold, MD Chairman, Technology Committee: European Society for Endoscopic Surgery
  • Olivia Hallisey Grand Prize Winner, 2015 Google Science Fair

Disrupting Clinical Practice: Todd Huffman Founder & CEO, 3Scan

Future of Cancer

  • Marty Tenenbaum, PhD Founder, Cancer Commons and Chairman & Founder/Chairman, CommerceNet
  • Sangeeta Bhatia, MD PhD, Director of Laboratory for Multiscale Regenerative Technologies, MIT
  • David Roberts, MBA, Former Special Agent, Business and Technology Disruption Expert

IMG_20161009_121012
The other cool thing that happened on day 2 is that I received an award: the Precision Medicine Impact Challenge Award launched by the White House Initiative on Precision Medicine and awarded by the State of California, presented by Elizabeth Baca, MD MPA, from the California Governor’s Office.
IMG_20161009_133001

Re-designing a NASA interface

interface

I am interested in many things. One of the main ones is technology. And within technology, software development to view telemetry data in different ways, within the same application.

Answering NASA’s call to help contribute to the exploration of the solar system, I got access to their next-generation mission control framework being developed at the NASA Ames Research Center in Silicon Valley being used for mission planning and operations in the lead up to the Resource Prospector mission, and at NASA’s Jet Propulsion Laboratory to view data from the Curiosity Rover.

Although I do not have much “spare time”, I have been tinkering with composing and modifying screen layouts, bringing together various telemetry objects and other object types in a single screen, following some basic design principles, as outlined in a book I have read recently: Designing for Emerging Technologies – UX for Genomics, Robotics and the IoT, by Jonathan Follett (Editor) published by O’Reilly.

Still a “work in progress”, but I hope my contributions help.

Talking to Prof. Church about machine learning applied to genomic research

During my flight to Boston I read “Regenesis”, the interesting genomic science book by Professor George Church, which was a gift from my friend Dr. Raminderpal Singh.

George, Raminder and Jorge 2016 Boston

On Wednesday evening I had a very interesting conversation in Boston with both of them. Neither of them needs an introduction in the genomics world, but for those of you outside the field:

  • Raminder is Vice-president at Eagle Genomics and Advisor at Kanteron Systems. He was previously Genomic Medicine Strategy Lead at IBM, where he was responsible for the Watson Genomics project.
  • George is a bestselling author, Professor of Genetics at Harvard Medical School and Professor of Health Sciences and Technology at Harvard and MIT. His PhD led to the first genome sequence and contributed to nearly all “next generation” DNA sequencing methods.

Since George’s lab work revolves around chip-DNA-synthesis, gene editing, stem cell engineering, super-resolution, molecular computing, dark matter and similar subjects, and since he has PhD students from Harvard, MIT, Boston U., and Cambridge, during the conversation I could not resist the opportunity and I asked him about de novo computational discovery of motifs.

It is an idea I had a few weeks ago while sailing from Saint Petersburg to Helsinki: what if we apply machine learning/intelligence (whether Random Forests or Hierarchical Temporal Memory) algorithms, or even better quantum computing, to look for sequence motifs (nucleotide or amino-acid sequence pattern) to help us predict and engineer structural motifs (chain-like biological molecules)? We could begin with those related to binding and folding, which could lead to an exponential advance in the field of information storage and synthetic biology. But that would be only the beginning. The possibilities and implications could be really far fetching. It would overflow the SFLD 😉

In a nutshell (graphical silly example), it would make it much easier to go from this:
to this:

And not only describe it, but also understand it and facilitate its application in de-novo engineering.

There are already over 100 software programs which try to do this programmatically (MEME, EXTREME, AlignAce, Amadeus, CisModule, FIRE, Gibbs Motif Sampler, PhyloGibbs, SeSiMCMC, ChIPMunk, Weeder, SCOPE, MotifVoter, MProfiler…). Weirauch et al. evaluated many in a 2013 benchmark. But what I am proposing is a lot more powerful, versatile, and quick than anything done before (as far as I know).

He mentioned some of the research work his wife (Harvard Professor Ting Wu, whom I also met in Boston) is currently involved in around Super-resolution imaging for chromatin folding, and evolutionary conservation, and told me “your idea is really interesting”.

Honestly, I usually can care less about what others think of my ideas (I’m a scientist, I value evidence and data, not “beliefs” or “judgements”) but I personally admire and respect his work, and agree with his views, specially on sharing knowledge and human genome editing, so his comment made my day and encouraged me to further pursue that hypothesis… someday. Right now in my spare time I am redesigning a multi-sensors data stream interface for NASA (pro-bono, unrequested… but that’s my idea of fun!).

Festival of Genomics Boston

June 28 and 29 I attended, along with my friend John Memarian, President & CCO of my company Kanteron Systems, the Festival of Genomics Boston, as a Microsoft Genomics Group partner.

Although the show was small, it was a great opportunity to network with industry and academic experts (from Harvard Professors to Illumina executives) and learn.

From scientific posters to the latest sequencing technologies, from robotic arms to genomics experiments in space, it was great #geekfun.

Ultimate Father’s Day gift: building a Picade with my son

For Father’s Day (we live in London, so we celebrate it today, unlike in Spain which is March 19) my wife gave me the “Ultimate Father’s Day” gift, from TechCamp UK. [Thank you, love!]

It consisted of a workshop with other father-son / father-daughter “teams”, held at the Iron Yard (The Leathermarket – London), where we built a desktop arcade machine in 5 hours (including lunch break), following the directions from Tom and Tom, using the Picade set, setting up and using the Raspberry Pi, custom OS, emulators, ROMs, loudspeakers, power supply, LCD screen, etc:

Not only we had a lot of fun and bonded through the “hard” work (especially getting all those nuts and bolts and cables in their little places!) of putting together the mini arcade machine, but my son also learned a few very valuable lessons, like being patient, not being shy, following directions carefully, and the main one, overcoming adversity: our board had a loose connector, which had to be soldered, and when we finished setting up the arcade… the screen was upside down! It took some thinking and engineering to get it straight up.

To top it all off, we got to take the arcade home, so now, if you will excuse me, I NEED TO install the Super Mario Bros. ROM and mash some buttons old style 😉

Invited to InfoSecurity Europe

Today I was invited to attend InfoSecurity Europe, Europe’s largest Information Security industry event.

As always, it was interesting to have a chance to catch up with this rapidly moving field, and a great opportunity to chat with old friends.

Apart from gimmicks (VR everywhere, car racing and helicopter simulators, giant robots, etc), swag (all kinds of Star Wars and other Sci-Fi related giveaways, from toys to t-shirts) and junk food (from candy to icecream to chips, the booths did not have healthy alternatives, although the food vendors did), the most interesting part of these events is always the talks, specifically the hands-on demos.

This time my favorite was a live car-hacking session. It’s SO easy I feel like… no, I will not go back to the dark side. But it seemed so much fun I might do it as “white hat”!

Invited with my son to Intel Buzz videogame developer workshop

Today I was invited, along with my son, who at 14 has been a videogame developer for years, to attend the Intel Buzz videogame developer workshop. It was not only a lot of fun, but WONDERFUL to attend with him!

Although a small event, it ended up being extremely interesting, with an area to try indie games and new technologies, and a long list of talks and panels, including one-on-ones.

Almost all of the indie games showcased were really good. My favourite was Elise: Unpainted Memories:

The speakers were amazing, like:

  • Ed Fries, Co-founder of the Xbox Project and Microsoft Game Studios
  • Kate Edwards, Executive Director of the International Game Developers Association (IGDA)
  • Oscar Clark, Evangelist for Everyplay & UnityAds, Unity Technologies
  • Penka Kouneva, Game Composer (Prince of Persia, Transformers), leader in Game Audio
    Will Eastcott, CEO and co-founder of PlayCanvas

The talks and technology were really interesting, and the games and technology we tried (like the Rovr) were super cool. But the two main conclusions are: VR is all the rage, and it’s going to be everywhere soon (coming to Chrome for Android in October!), and there were a lot of women attending (which is great, and hopefully a sign that gender equality is finally arriving to the tech industry).

A couple days in Zürich

I spent Wednesday evening and most of Thursday in Zürich.

On Wednesday I had dinner with some business partners; “business as usual”.

But on Thursday, after my business presentation to potential customers, I had the very rare and exclusive opportunity to visit one of the main data centers in Switzerland. Here are some impressive facts about them:

  • they host 1/3 of Swiss banks data
  • internet traffic = 40% of Switzerland’s internet traffic
  • energy bill = 2 million Swiss Franks per annum
  • 2 different energy suppliers from 2 different access points, with preferential oil supply in case of a failure (full reserves for 5 days for the generators)
  • almost 50 telecoms suppliers, from many different countries, providing direct access for their customers worldwide
  • RFIDs paired with 3D fingerprint scanners which measure the fingerprint but also the morphology, pulse and temperature
  • separate isolated room to open packages, to minimize the risk of fire
  • single person magnetic doors
  • temperature, movement, and sound sensors
  • double-gated entrance even to the parking lot!
  • building-within-building construction to avoid physical damage from a truck, explosives, missiles…
  • near the airport for easy access, but out of any flight path to minimize the risk of airline accident

Even most Hollywood movies don’t portray these high-security technology facilities accurately!