Open Presenting

pythonby belgianchocolate

Publishing On OpenWetWare – Lessons Learned 4 – Presenting:Python
[Via Programmable Cells]

This is the fifth report of the ‘Publishing on OpenWetWare’ series. In brief, I am writing an article on OWW from start to finish: initial writing -> collecting comments -> publishing on -> presenting at a conference. For other articles, see one, two, three, four. In this report, I’ll share my experiences in presenting the work at Pycon 2008.

This is the most recent part in a continuing series by Julius Lucks about publishing on OpenWetWare, an example of Open Science. Initially, OpenWetWare was a great site to find protocols of all sorts. It has been expanding very rapidly to incorporate many facets of Science 2.0. This is one such. It led to a presentation dealing with his work and you can read the ‘paper’ dealing with his topic: Python All A Scientist Needs. Python is the programming language used here and it presents many advantages useful for scientists. It includes a special package, BioPython, just for biologists, which is supported by the Open Bioinformatics Foundation. So, we see an entire network of Open Source organizations that produce tools that not only make their work easier but also the work of others. By embracing these tools, one can engage the entire network and help use all the knowledge contained in it to help solve problems.

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TEDTalks are the best

TEDTalks: Jill Taylor (2008):
[Via TEDTalks (video)]

We are still working on the website to permit embedded Flash. Until we do, you will have to click the link above to see Jill Taylor’s presentation.

Neuroanatomist Jill Bolte Taylor had an opportunity few brain scientists would wish for: One morning, she realized she was having a massive stroke. As it happened — as she felt her brain functions slip away one by one, speech, movement, understanding — she studied and remembered every moment. This is a powerful story about how our brains define us and connect us to the world and to one another.

This is a great presentation. Some science. Some personal experience. The TEDTalks offer great examples of how to present difficult subjects. There are some with pretty standard approaches but they are often the best of their type. And, thanks to the Internet, we do not have to be attendees in order to see this.

But some of them display a unique method of presenting and are very useful for gaining a better understanding of HOW to present. Check out this one from Larry Lessig.

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Bumps in the road to Science 2.0

dunesby Hamed Saber

Why Web 2.0 is failing in Biology
[Via Bench Marks]

Last week I gave a talk at the American Association of Publishers Professional and Scholarly Publishing (AAP/PSP) meeting in Washington, DC. I was part of a panel discussion on “Innovative and Evolving Websites in STM Publishing” along with representatives from the New England Journal of Medicine, the Royal Society of Chemistry and the American Chemical Society. While the other talks were a bit more evangelical, or mostly presented a look at new technologies that had been incorporated into the societies’ own journals, I tried to be a bit more practical, taking more of a hard look at what’s currently being tried, whether it’s succeeding and the reasons behind that success/failure. I’m posting my talk below, in hopes of receiving further feedback. This talk was delivered to a room full of publishers, so it’s directed with that audience in mind. In a few months, I’m giving a similar talk to a meeting of scientists, the users of these sites rather than the creators. So I’d love to hear from users as to your thoughts on how Web 2.0 is serving your needs.


There are some very important points in this article. Essentially, researchers will not just jump on these new technologies. They do not have the time to learn. They do not see the reasons why. Now most of the difficulties described here deal with academic researchers and the problems with using Web 2.0 ‘in the wild.’ They have concerns about priority, the effect on tenure, Facebook makes no sense to their work, etc.

Many of these problems stem from the fact that no scientist can see what is in it for them. Few of them do anything that does not make their life easier, as do most people. An example – researchers have little time but they always (or at least the good ones do) take time to put together a good lab notebook. This is not time used for experiments but everyone knows how vital it is to a career. So they take the time to do it right.

Similar things can be done with Web 2.0 approaches. Make them understand the personal benefit. For example, most scientists will think a blog is useless and a waste of time. But show them how to combine newsfeeds from scientific journals with a blog, and now they can have a very quick repository of interesting/important papers that they need to read. They can ‘clip’ these articles rapidly and then come back to read them at their leisure.

This directly affects their productivity since staying current with the literature is normally a time-consuming endeavor. I can scan over 1000 articles in 30 minutes and put the ones I want on my blog. The researchers that do this will be ahead of those that do not. But they have to be shown the direct personal benefits first.

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Something to watch for at any presentation

volcano by Clearly Ambiguous

A Groundswell at SXSW: How The Audience Revolted and Asserted Control:
[Via Web Strategy by Jeremiah]

For the second year, I experienced the SXSW Interactive Festival, an event attended by thousands who have love for media, the web, and gadgets. SXSW is a bubble of the tech elite assembling, in many ways it’s a glimpse into the future, exposed on a Petri dish today.

[A Groundswell Occurred at the SXSW Interactive Festival as the Audience Revolted And Took Charge]
Last year, Twitter gained traction at SXSW 2007, this year, it fully ramped up to be one of the most prominent and power shifting tools of the festival –we witnessesd a Groundswell. What’s a Groundswell? It’s a social trend in which people use technologies to get the things they need from each other, rather than from traditional institutions. Dan Fost, writing for Fortune Magazine reports that this is Social media is putting an end to the passive role attendees traditionally play at business gatherings.


The ability of attendees to communicate with one another in realtime during a presentation will become more and more prevalent. I expect few scientists currently use Twitter during a talk but the ability to carry on back channel communications will make its appearance some day. The example at SXSW was a little more raucous than I would expect to see at the annual meeting of the AMA but it might be as rancorous.

Part of the problem here was the relative anonymity of the chatter. That is, the speakers were not seeing any of this discussion and so were unaware of it direction. I would expect that as we progress, others will monitor the channels and help keep the presenter aware of just what is happening. How about tweets posted on a monitor for the speakers?

In my personal experience, I have seen some very creative approaches used by the audience to produce some wonderfully useful items. At the second ETech meeting several of us used a program then called Hydra, now called SubEthaEdit, that allowed users to create a collaborative document in realtime using WiFi to connect. Four or five of us would take notes, often catching items others would miss. Someone would add Web links for relevant items. We could write in comments, etc. and create a very rich document that was much denser in its information content than if any of us had written it by ourselves.

I am surprised more of this is not happening at meetings or even in class. Study groups could produce very robust documents for the group. I would imagine that there even might be a market for these sorts of notes, for those who slept through the presentation.

So audiences can be more than just unruly.

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Change the world slowly

jets by foxypar4

John Tropea: “tools are the conduit for this culture change”
[Via Grow Your Wiki]

John Tropea says people need to understand why they should use Web 2.0 tools in organizations, not just “because everyone else is doing it so I need to as well, and I’ll just use this recipe approach.”

Web 2.0 is not really something completely different. It involves new tools that help us do what we already want to do, just with greater ease. But people do not normally make such changes in their behavior without some real knowledge of the benefits AND difficulties. It is important to help them leap the chasm between the old way and the new way. But it is only a difference in doing things.

Of course, once they start doing the old things in a new way, they will also discover how to do new things in a new way. Just as TV started out as visual radio then became its own medium, so will Web 2.0 technologies start out as something similar to email or chat before revealing its own uniqueness. You won’t get people to use it though by saying it is unique. You have to show them how it will make their life easier.

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The Government and Web 2.0 technology

pigs by artct45

Agencies Share Information By Taking a Page From Wikipedia
[Via The Washington Post]

The government seems to be jumping on Web 2.0 techniques faster than many corporations. Here they used a wiki to compile a list of earmarks. They accomplished in 10 weeks what would have taken 6 months before. This now makes it much easier to see where the pork is coming from. They maintain the wiki behind a security wall so that only invited members can post. This is easily done and can be applied to almost most wikis. The ability to allow rapid information flow and transformation makes a wiki a powerful tool. And if the Government can do it, and see immediate positive effects, then so could most organizations.

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Disruptive Leaders from the Gaming World

by aeu04117

Are Gamers Born or Made?
[Via Conversation Starter]

In an online response to our recent essay “The Gamer Disposition” and its discussion of leadership in MMOGs, Joi Ito wondered whether playing games creates the gamer disposition (bottom line orientation, embracing diversity, thriving on change, seeing learning as fun, and marinating on the edge) or whether they simply tend to attract the kinds of people that already have that disposition.The question Ito poses is the 21st century equivalent of the age old problem: Are leaders born or made? Or perhaps, in our context: Are gamers born or made.


Read the entire article to get a flavor for how management leaders coming from a gaming background attack problems in very different ways than old style, GE approaches. Leaders of online guilds view management problems as quests to be solved, not a specifications that they have to follow.

… he believed that part of solving the challenge/quest was finding the resources to accomplish the task. From his success in the game world he was confident that he could find skilled people and attract them to work on his quest no matter where they were in the corporation. Such attitudes, while disruptive in most corporations (jumping over silos and seducing folks to work on YOUR problem) are commonplace in games.

Businesses will have to get used to the gaming mentality as more and more people are entering the workforce with this sort of ‘experience.’ These leaders will gravitate to the companies that permit them to lead. Interesting that people learn management skills while playing a game.

Great photo resource

Galaxy Edge On by The Hubble Heritage Team (STScI/AURA)

Images help give a website a nice look. They break up the text and provide some visual interest. Flickr is a great spot to get images. There are a huge number that are covered by the Creative Commons license that can be used. But it is nice to find others.

The Hubble Heritage Image Gallery is another great site. Excellent images of objects in space. You can simply place these photos onto your web page and provide proper attribution. This is one of the great mashups on the Internet. Great photos taken by people can get spread around the Internet in ays that enhance both the user and the photographer.

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Scientists as cyborgs

Video @ the bench
[Vie Free Genes]

I saw the movie I Am Legend this weekend, and although it wasn’t exactly a ringing endorsement of synthetic biology (re-engineering measles is a bad idea, apparently) Will Smith’s character did have a slick lab in his basement. Good to see a little Garage Biotech in action.One component of the lab they made heavy use of was a video lab notebook. I assume this was done since Will Smith scribbling in a paper lab notebook wouldn’t have had quite the same cinematic effect. However, getting video into the lab will be important for democratizing biological engineering. A lot of the barriers to would be bio-hackers lay in the difficulty of learning biological protocols from texts. New graduate students benefit enormously from hands-on learning with a mentor in their early days in lab, and without this visual teaching getting booted up in the lab is extremely frustrating.

will.JPGNew science video sites like Jove and suffer because labs aren’t really equipped to capture video. So at best you’ll be able to disseminate talks, but video protocols are going to be very hard to pull off. I’ve been thinking about video lab notebooks / protocols since Tom Knight brought up some clever ways you might set your bench up to accommodate video capture (cameras in various spots, foot-petal control, and smart ways to handle the data). A more nerdy looking way to do this (no offense to Will Bosworth who used to work around the Endy Lab) is the head-mounted video camera described by Saul Griffith in Make magazine.

There are also some wireless web-cameras that might make your setup cheaper. If anyone is doing a good job of taking video at the bench, please let me know about your setup.

Video use in social media will be explosive when the tools get more mature. Will they be a major way that research is communicated? Maybe not always but I visited the Seattle Science Foundation last week and saw what medical theaters can do when hi-def video is built into the infrastructure. Almost everything can be transmitted/archived on video. How will things change when we really can archive everything?

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“fun, easy-to-use, collaborative applications” …in the workplace?:

Sarah Perez has written an excellent piece on the new trend of Technology Populism – where “more and more people are functioning as their own IT department at work.”

More than anything, IT Managers need to realize that the power of individuals to provision their own applications, information, and social networks is a trend that’s unlikely to stop. They can block sites on their firewall, but as users venture out on laptop computers beyond the company’s walls, those sites become accessible again.

It’s like a hydra – cut off one head, proverbially speaking, and three more will grow it its place. People will use what they want to use.

For an IT manager to successfully balance the risks and rewards of technology populism, they must first embrace the trend to move forward, then they must address their particular company’s exposure levels.

Some IT managers dig their heels in and refuse to embrace the new trend.

But I think that group is smaller than one would think. Many more IT managers try to address and manage exposure levels – but the problem is they jump right to that step without first putting out the message that they embrace the new trend, and I think that leads people to think they don’t.


Read the whole article. There is a nice graphic dealing with the percentage of companies planning on using social media. It appears that many companies will be using these technologies without even knowing it. They are just too easy for any employee to implement. The take home message – a company may feel that it knows what is happening but often it employees are using the new tools whether the company plans to or not. Better to grab the tiger’s tail and hope to keep up than to just close your eyes. Because, very often, that tiger takes you on a trip that adds real value to the organization.

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