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!

Invited to the UK-China Hi! Technology event in London

For reasons beyond the scope of this post I was invited to participate in the UK-China Hi! Technology event in London.

The event was well attended by a large number of entrepreneurs, funds and investors from the UK and China.

The highlight of the event, for me, other than a couple of really interesting contacts, was to see all these suited-up people lining up to try the VR sets (HTC, Oculus, Hololens, etc). The clear winner was Robot Recall for the Oculus platform.

Spare time fun: protein structure analysis of mutations causing inheritable diseases

Most people I know would not consider protein structure analysis of mutations causing inheritable diseases “spare time fun”. Then again, most people I know don’t think I am like most people they know.

This week I’m a “single-dad”, since my wife is traveling. So my spare time right now is almost non existent. Nevertheless, the thought of mutating a Proline into a Glycine at position 22 intrigued me, so I spent a few minutes simulating it. Here is what I found out:

Method

The 3D-structure of my protein of interest was obtained from the UniProt database using Reprof. The structural information was obtained from the analysis of PDB: 3NIR. Annotations were obtained from UniProt entry CRAM_CRAAB.

Amino Acids

I was interested in the mutation of a Proline into a Glycine at position 22.

The figure below shows the schematic structures of the original (left) and the mutant (right) amino acid. The backbone, which is the same for each amino acid, is colored red. The side chain, unique for each amino acid, is colored black.

 mutates into 

Each amino acid has its own specific size, charge, and hydrophobicity-value. The original wild-type residue and newly introduced mutant residue differ in these properties: the mutant residue is smaller than the wild-type residue, while the wild-type residue is more hydrophobic than the mutant residue.

Variants

A mutation to “S” was found at this position, which differs from the mutation I was simulating. The effect of this variant is annotated as: In isoform SI.

Conservation

The wild-type residue is not conserved at this position. Another residue type was observed more often at this position in other homologous sequences. This means that other homologous proteins exist with that other residue type than with the wild-type residue in my protein sequence, but the other residue type is not similar to my mutant residue. Therefore, the mutation is possibly damaging.

Domains

This residue is part of an interpro domain named: Thionin IPR001010

The mutated residue is located on the surface of a domain with unknown function. The residue was not found to be in contact with other domains of which the function is known within the used structure. However, contact with other molecules or domains is still possible and might be affected by this mutation.

Amino Acid Properties

The wild-type and mutant amino acids differ in size. The mutant residue is smaller than the wild-type residue. This will cause a possible loss of external interactions.

The hydrophobicity of the wild-type and mutant residue differs. The mutation might cause loss of hydrophobic interactions with other molecules on the surface of the protein.

Images

Overview of the protein in ribbon-presentation. The protein is coloured by element; α-helix=blue, β-strand = red, turn=green, and random coil=cyan.

Overview of the protein in ribbon-presentation. The protein is coloured grey, the side chain of the mutated residue is coloured magenta and shown as small balls.

Close-up of the mutation. The protein is coloured grey, the side chains of both the wild-type and the mutant residue are shown and coloured green and red respectively.

Close-up of the mutation (seen from a slightly different angle). The protein is coloured grey, the side chains of both the wild-type and the mutant residue are shown and coloured green and red (not show from this angle) respectively.

Close-up of the mutation (seen from a slightly different angle). The protein is coloured grey, the side chains of both the wild-type and the mutant residue are shown and coloured green and red respectively.

Movies

Close-up of the mutation. Both the wild-type and mutant side chain are shown in green and red respectively. The rest of the protein is show in grey.

Close-up of the mutation, same colours as animation 1. The animation shows alternating the wild-type side chain and the mutant side chain.

Citation

Protein structure analysis of mutations causing inheritable diseases. DOI: 10.1186/1471-2105-11-548. PubMed: 21059217.

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.

Valencia (Spain) VC flows

Adam Gilfix, Brian de Luna, and Luke Heine, with the help of Dealroom.co, have created a very interesting data visualization tool for Venture Capital (VC) flows.

I know for a fact and from experience that VC activity in places like Silicon Valley, NY, Boston, or London is big. But even when I go back home (Valencia – Spain) for the holidays, there are all kinds of “VC” events, news, meetings, spaces… which, given the conservative and provincial nature of the “Valencian Investors” I have met, surprises me.

So I decided to check out Valencia (Spain) VC flows. Unsurprisingly, those “flows” (both inbound and outbound) are quite recent, very very small, extremely limited in geographical reach, and conservative in industries. See for yourself:

View post on imgur.com

View post on imgur.com

View post on imgur.com

Several caveats, though:

  • The data may not cover ALL VC activity in the region
  • Some activity may be wrongly identified (for example, there is a transaction coming from “Valencia – Venezuela”, which could be a coincidence, or most likely a data collection error)

My company has been named “Top Scaleup in the UK”

For second consecutive year, my company has been named “Top Scaleup in the UK”. This means that we are growing fast, and also that I get invited to cool events. One of those events was a reception and a ‘Ten Years From Now’ series of keynotes at the Royal Institution of Great Britain, another one a mentoring session at London’s City Hall, and another one a series of talks at Google Campus. Some of the people I met at those events were:

  • Brian Forda, Crypto Currency Professor, MIT
  • Maria Contreras-Sweet, Director, USA Small Business Administration
  • Megan Smith, US Chief Technology Officer, White House Office of Science and Technology Policy
  • Obi Felten, Director, Google X

Microsoft Future Decoded 2016

November 1 I attended Future Decoded, the annual event where Microsoft and Partners present their forward looking products and concepts.

Besides some cool “event attractions” (like the Back To The Future Delorean, seeing how data is not completely deleted even if you deep freeze a hard drive, the Bloodhound record-breaking car, or seeing the inside of a Rolls Royce plane turbine), the key for me was to be able to demonstrate my company’s software running on an amazing 84” Microsoft Surface Hub, and attending the invitation-only Microsoft Executive Party at the Sunborn Yacht Hotel.

Exponential Medicine Conference San Diego day 4

Tuesday, October 11th, was day four, and last, at the Exponential Medicine Conference in San Diego.

Some of the talks I enjoyed the most:

Exponential Thinking & Future Predictions: Ray Kurzweil Co-founder & Chancellor, Singularity University

Exponential Entrepreneurship:

  • Zayna Khayat, PhD Lead, MaRS Health and Director, MaRS EXCITE
  • Stephanie Marrus, MBA Entrepreneurship Center Director, UCSF

Investing In The Future: Vinod Khosla Founder, Khosla Ventures

Visualizing the Future of Medical Education, from VR to the OR:

  • Stefano Bini, MD Professor of Orthopedics, UCSF
  • Stephen Swensen Medical Director- Leadership and Organization Development, Mayo Clinic

Synthesis- From Imagination to Innovation to Impact
Kevin Wildenhaus, PhD Behavioral Science Lead: Janssen Disease Interception Accelerator, Johnson & Johnson

And right after that, I left for the airport.

Here you can see more photos from the event.

Tea with Peter Diamandis and dinner with Vinod Khosla

Monday, October 10th, I had the pleasure to have a chat with Peter Diamandis at a coffee (tea for me, thank you) break.

IMG_20161010_134626

He was very interested in talking about my company (Kanteron Systems), as we have developed technology that can really help some of his investments in Precision Medicine and Longevity.

Even more interesting than talking about investments, it was to know a little bit the man behind the legend.

Something similar happened when I had dinner on the beach, that same day, with legendary investor Vinod Khosla.

Exponential Medicine Conference San Diego day 3

Monday, October 10th was day 3 at the Exponential Medicine Conference San Diego.

For me the highlights were:

Bold Innovation: Peter Diamandis, MD Co-Founder, Singularity University and Founder & Chair, XPRIZE

Redesigning Care: Tony Young, PhD FRCS National Clinical Director for Innovation, NHS England

Bakul Patel, MBA Associate Director of Digital Health, Food and Drug Administration/Center for Devices and Radiological Health

Getting the xMED Scrubs Photo on the Beach, with an awesome drone:

The Brain and Beyond

  • Divya Chander, MD PhD Anesthesiologist/Neuroscientist, Stanford University
  • Arshya Vahabzadeh, MD Psychiatrist, Harvard Medical School
  • Anthony Bossis, PhD Clinical Assistant Professor- Department of Psychiatry, NYU School of Medicine

Off the Planet, Remote Medicine: Scott Parazynski, MD Managing Director, Apogee Interests & 5 Time NASA Astronaut (Retired)

Security & Privacy Threats in Healthcare (And What to Do About It): Marc Goodman, Resident futurologist at the FBI, Policy Law and Ethics Faculty Chair, Singularity University and Founder, FutureCrimes

The day ended with dinner on the beach, and a beach party, with bonfire and drum circle.