Archive for the ‘IT’ Category
Posted by attilacsordas on September 18, 2008
There is a nice initiative now in Budapest dedicated to the present and future of high technology: a new private university momentarily dubbed as Aquincum Institute of Technology (AIT) will be built near to the Graphisoft Park in Óbuda (Aquincum) concentrating on competitive information-/biotechnology (mainly bioinformatics) education and entrepreneurship.
The main instigator of the project is Gábor Bojár, founder and CEO of the most successful Hungarian software company, Graphisoft.
According to this source:
“The company aims to become the global leader in building-architectural software solutions, hence it must found the training of professionals on a business basis, Bojar said. The new school is to be opened in 2010.”
Mr. Bojár convinced world-class Hungarian scientists and businessmen like Wolf-prize winner discrete mathematician and computer scientist László Lovász, inventor and architecture professor Ernő Rubik, former Office guru, intentional programmer and space tourist Simonyi Charles and scale-free network theorist Albert-László Barabási amongst others to back the idea of a profit-oriented technology university sustained by the market itself.
It’s not too hard to recognize some particular Silicon Valley virtues or models behind the idea of an university like AIT let’s just think about the innovative environment at Stanford, intellectual and entrepreneurial home of the HP, Sun Microsystems and Google founders. What I have in mind here concerning the biotechnology part is The California Institute for Quantitative Biosciences (QB3) which is ‘a cooperative effort between the state of California, the University of California campuses at Berkeley, San Francisco, and Santa Cruz, and industry and venture capital partners’.
The idea can be traced back to a San Francisco dinner Read the rest of this entry »
Posted in bioinformatics, biotechnology, Budapest, business 2.0, education, Hungary, industry, IT, IT&BT, technology | 13 Comments »
Posted by attilacsordas on September 16, 2008
Following Matt Cutts’s tweet I am now writing my blog post using the CrossOver Chromium browser which is a Mac and Linux port of the open source Chromium web browser. Google Chrome (Windows-only so far) is built with open source code from Chromium that means I have now a functional Google Chrome clone under Leopard on my MacBook. This is almost the same experience just like 2 weeks ago. I can use the omnibox, the new home tab and the very clever tab arhictecture amongst others but first of all the browser is now more or less integrated into my customized OS X environment and that is a big advantage. There are of course, inconveniences like crashes and problems with the shortcuts due to the Windows – Mac crossover solutions (which can be modestly modified with Preferences).
Read the rest of this entry »
Posted in Apple, geek, google, googleplex, IT, open source, technology | 13 Comments »
Posted by attilacsordas on June 1, 2008
Sergey Brin, Google co-founder is a very interesting man. His story is the number one immigrant success story in the USA today, I dare say. I have 2 Brin videos to show you today:
In the first one, Sergey demonstrates mobility in 2000 in 3 ways with his ‘faint accent that is no longer identifiably Russian’ (I really like this presentation as you can learn many things on how to give and not to give a talk):
In the second video Sergey speaks in his native language, Russian but with a “huuuge american accent” as a Russian colleague of mine wrote to me in an email. Read the rest of this entry »
Posted in career, celebrity, google, googleplex, innovation, IT, personal, presentation, SergeyBrin, Silicon Valley, technology, USA, video | 1 Comment »
Posted by attilacsordas on May 14, 2008
Just a simple filtering & highlighting & regurgitating for you based on Andy Oram’s post apropos of the opening of a larger Cambridge, Massachusetts Google office : Why open source developers can be more productive, and other tales from a Google open house
Along the lines of self-motivated employees, I asked a manager whether most of their new products came from the individual employees or from management. He expressed the conviction that most innovation in most companies comes from individual employees. Where management can help is in finding effective places to fit new features into the organization and product line.
Google found that releasing too many products prevented the public from learning about them and adopting them. Adding a feature to an existing product such as Gmail or Blogger could mean that millions of people adopt it, whereas releasing it as a stand-along product might limit adoption to a few thousand.
The question for me is always how these experiences can be compared and applied to the biotech industry, in this case I am curious how biotechnological innovation is going in the profit sector outside academia. So if you are working at a biotech startup or at a big pharma please share us your opinion (anonymously if you like) in the comments on the nature of innovation at your company!
Posted in google, googleplex, innovation, IT, IT&BT, technology, USA | Comments Off
Posted by attilacsordas on April 21, 2008
Wow, I guess it’s time for me to move into the stock market business! Here’s the story via David Bradley’s tweet: Julie Kent, Search Engine Journal, April 21st, 2008: Google Wants to Index Genetic Information, Invests in Second DNA Start-Up
In 2007, Google made headlines when they invested $4.4 million in 23andMe, a genetic screening start-up company began by Anne Wojcicki, the wife of Google co-founder Sergey Brin, and a business partner. But if you thought that was Google’s only interest in genetics and DNA, you’re wrong. Google has also been investing in a second DNA start-up called Navigenics, which for $2,500 and a small bit of saliva will provide you with genetic test results delivered securely online containing information about the likelihood for 18 medical conditions.
What’s really funny here is that I predicted this investment last Friday, on the 18th, on Twitter. The original idea was Aaron Swartz’s Google thought experiment: Imagine you were suddenly put in charge of Google. What would you spend your time doing? I came up with this answer (picking Navigenics because of ther profile and location) on behalf of Sergey Brin:
The whole tweetstream: Read the rest of this entry »
Posted in 23andMe, Bay Area, biotechnology, business 2.0, future, google, googleplex, IT, IT&BT, medicine, personal, personalized genomics, Silicon Valley, technology, Twitter, USA | 6 Comments »
Posted by attilacsordas on March 28, 2008
Building and using low budget but high tech devices at home is a main motivation behind hacking. A Harvard Chemistry Research Group now created a microchannel producing device using a Hewlett Packard 7550A Graphics Plotter (see some eBay prices) to perform a diagnostic protein assay with it amongst others. /See my SciFoo microfluidics coverage./
According to the current Nature by Tim Lincoln:
“The system works like this. By replica moulding, the pens of the plotter are replaced with PDMS versions that can deliver various types of ‘ink’. The purpose of the ink, when cured, is to create channels in a filter-paper substrate, and after experimenting with the possibilities Bruzewicz et al. found that a syrupy mixture of 3:1 PDMS:hexane did just fine. Having chosen the appropriate paper, the trick then is to use the plotter to draw channel shapes, with the PDMS syrup penetrating the full depth of the paper to create water-tight chambers in various patterns.”
Hardware-Software Specs from the supporting information:
• Computer: Dell Dimension 4100, Pentium III Processor (1 GHz)
• Plotter: Hewlett Packard 7550A Graphics Plotter
• Operating System: OpenSuSE Linux 10.1, Novell Corporation. Available for free download
• Additional Software:
1. Inkscape – vector drawing program, for design of channels. Included in OpenSuSE, also
available for free.
The HP Computer Museum highlights this particular plotter: Read the rest of this entry »
Posted in biodiy, biohacking, biotechnology, diy, gadget, geek, IT, methods, open science, open source, Sci Foo, science, technology, USA | 5 Comments »
Posted by attilacsordas on January 28, 2008
According to the Wikipedia approved rumor by the AT&T boss: “A new version of Apple’s iPhone will be introduced in 2008 that is capable of operating on faster 3G cellular networks.” Besides the 3G support I have some other expectations (at least 6 should be satisfied) too in order to become a next generation iPhone upgrader:
- built in RFID reader/writer: because I’d like to buy and order without standing in line. Also a bit experimental RFID hacking with things around me, like opening the hotel room with a cream cheese box must be fun. (I would wire the RFID modul in the place of the Bluetooth modul on the motherboard) see: Will the Apple iPhone be RFID powered?
- video out to use the iPhone with projectors: giving presentations on science conferences and seminars with my SciPhone and watching movies back at home with my wife.
- GPS (although I am quite satisfied with the Google Maps Mobile): in the car and on the bike.
- video recorder: basics
- video telephone: just for fun
- longer battery life: a must
- solar panel: for climate change
- Skype enabled: do I need to explain it why? Read the rest of this entry »
Posted in Apple, gadget, iPhone, IT, SciPhone, technology, USA | 1 Comment »
Posted by attilacsordas on October 22, 2007
The biggest impact of the Austin Maker Faire on me was that yesterday I bought an open source, CC licensed Arduino microcontroller and a breadboard for building prototype electronic circuits. I am a total rookie in home electronics but I thought it’s never too late to learn completely new things with the help of our extended memory, the web.
In the long run I’d like to utilize my microcontroller (or the acquired knowledge) for biological purposes in the lab and not just blinking LEDs.
Have you heard of any quality biotech-biology based community (blog, forum, network) specialized in electronics or coding for researchers, online?
Links: How to buy
MAKE Arduino Archives
Posted in technology, biotechnology, IT, MAKE, diy, USA, IT&BT, geek, gadget, science hacks, education | 5 Comments »
Posted by attilacsordas on September 25, 2007
Google’s Palimpsest project, once realized (in the near future) has the potential to change the way science is done by accepting gigantic (raw?) data sets from all disciplines and making them open and free (including dark data?). Jon Trowbridge from Google Inc. had a presentation on SciFoo, 2007 at the Googleplex not documented well, but you can download his slides on the project that was presented at XTech 2007 in Paris, this May: Making Massive Datasets Universally Accessible and Useful Presentation. You are not restricted to the zip file as Jon kindly gave a permission to publish his slides with SlideShare here. From his intro: This talk will discuss a project underway at Google to collect and distribute large scientific datasets using a 21st century “Sneakernet”: multi-terabyte disk arrays shipped via FedEx and other common carriers.
The project is strictly non-profit, but fits well with Google’s mission.
Scifoo: Google and large scientific datasets
Google helps terabyte data swaps
Posted in data, google, googleplex, IT, Sci Foo, science, science slideshows, SciFoo, technology, USA | 43 Comments »
Posted by attilacsordas on August 29, 2007
I’ve activated my iPhone in a prepaid mode exactly for the reason of being flexible and switch to another network provider ASAP. So I do not have a 2 year contract with AT&T and I am happy to say that. The AT&T network and coverage is almost non exisiting in the 2 crucial places of my current life in New Orleans, United States: a., at home and b., at work. At home I must go to the street if I want to make a valid phone call with my iPhone, at work I must go to a special corridor at the edge of the building for the same reason. Next week I am going to England and it would be good to use my iPhone as a phone there. Nevertheless my iPhone is an integrated, hacked and essential part of my life. So what shall I do? Well, there are options it seems.
Something really new and interesting is happening, please read the links:
Wikipedia: George Hotz
Business Week: Why Apple Can’t Stop iPhone Hackers
Wired: Legal or Not, iPhone Hacks Might Spur Revolution
Slashdot (the comments): Can Apple + AT&T Shut Down iPhone Unlockers?
Posted in Apple, industry, iPhone, IT, lifehacks, technology, USA | Comments Off
Posted by attilacsordas on August 11, 2007
The Google Hacks book from O’Reilly was one out of the free goodies on the SciFoo last weekend. Hack #3 is Visualize Google Results with the TouchGraph Java applet that allows you to visually explore the connections between related websites. Of course I started with the term “scifoo” with the setting of filtering single nodes out of the network in order to see the separate groups of nodes behind.
Explore the detailed properties of the SciFoo URL cloud by double clicking the individual nodes in the network.
Posted in google, googleplex, IT, Nature Network, Nature Publishing Group, Natureplex, SciFoo, technology | 3 Comments »
Posted by attilacsordas on August 2, 2007
Posted in Apple, gadget, iPhone, IT, technology, USA | Comments Off
Posted by attilacsordas on July 25, 2007
This slide comes from the presentation of Google Fellow Jeff Dean on Seattle Conference on Scalability, entitled Abstractions for Handling Large Datasets. (The title Google Fellow seems to me as something similar in rank to a full professorship at Stanford.)
Here is the presentation itself embedded: Read the rest of this entry »
Posted in california, geek, google, history, IT, technology, USA | 1 Comment »
Posted by attilacsordas on July 24, 2007
I like Google and Apple products, but my expectations are focusing on how these products can help and facilitate me as a scientist, especially as a biomedical research scientist. With the Science on the iPhone test series I’d like to examine in details how proper and user friendly is the iPhone as an ultimate portable, mobile, convergent handheld gadget (or at least the first version of that line) for scientific purposes based on real experience. Briefly: can we use it as a SciPhone?
Amongst others I’ll concentrate on the following: the passive, science consuming opportunities like text reading, photo, presentation and science video watching and the active, science-making issues like writing texts, making photos and giving presentations.
Also I’d like to take a look on how the iPhone fits into the frame of the present scientific web, and how good is for scientific communication. (Photo: my bench this afternoon.) Read the rest of this entry »
Posted in technology, science, IT, science videos, USA, geek, Apple, gadget, lifehacks, science hacks, science publishing, iPhone, SciPhone | 5 Comments »
Posted by attilacsordas on July 23, 2007
Charlie Miller, Jake Honoroff, and Joshua Mason, members of the software security team at Independent Security Evaluators had discovered a vulnerability within two weeks of part time work and “developed a toolchain for working with the iPhone’s architecture (which also includes some tools from the #iphone-dev community), and created a proof-of-concept exploit capable of delivering files from the user’s iPhone to a remote attacker. The exploit is delivered via a malicious web page opened in the Safari browser on the iPhone.” Delivery vectors of the attack could be: an attacker controlled wireless access point, a misconfigured forum website, a link delivered via e-mail or SMS.
The professionals suggest 3 practices to diminish the iPhone’s vulnerability:
- Only visit sites you trust.
- Only use WiFi networks you trust.
- Don’t open web links from emails.
A preliminary technical paper called Security Evaluation of Apple iPhone is available.
Posted in Apple, gadget, iPhone, IT, USA | 1 Comment »
Posted by attilacsordas on June 12, 2007
The Natureplex (Nature Web Publishing Department on the second floor of a renovated warehouse with around 25 people near at King’s Cross, London) nerds are still busy: Scintilla, a science recommendation engine was launched based on aggregating science content from RSS/Atom feeds of various websites. How could Scintilla (check what the term scintillation refers to, it is a good name) be harmonized with other products of the NPG, like Postgenomic, Connotea, Nature Network…is a future question. For me it seems that the developers would like to convince me to use Scintilla feeds (in the long run) instead of Google Reader feeds when the content is about science in general and in details. The key word is personalization and personal filtering and in that respect maybe it is worth to think of Google’s personalized search trials and web history. More info (including the mail of Euan Adie, developer): Scintilla and Scintilla brings personalization to science
Posted in geek, IT, Nature, Nature Publishing Group, Natureplex, science, science journals, Search Engine, technology | 9 Comments »
Posted by attilacsordas on June 5, 2007
Wow, I feel fresh air, although I am not sure whether the following news is a beginning of any deeper changes or not: From Science Authors Guideline: “Because of changes Microsoft has made in its recent Word release that are incompatible with our internal workflow, which was built around previous versions of the software, Science cannot at present accept any files in the new .docx format produced through Microsoft Word 2007, either for initial submission or for revision. Users of this release of Word should convert these files to a format compatible with Word 2003 or Word for Macintosh 2004 (or, for initial submission, to a PDF file) before submitting to Science.”
Tips: Undernews: SCIENCE PUBS REJECT ARTICLES WRITTEN IN WORD 2007
O’Reilly Radar: Science and Nature rejecting Word 2007 Manuscripts
One commenter in Undernews said: “This isn’t just Science and Nature. All Wiley journals now include the instructions: “[Journal] does not accept Microsoft Word 2007 documents at this time. Please use Word’s “Save As” option to save your document as an older (.doc) file type.” So don’t think it’s a singular problem — I’m sure if you visited all the science journal publications, you’d find similar instructions as well.”
What can I say: Prepare for the age of Google Office manuscripts and figures! All you need is a gmail account.
P.S. I made an attempt to coedit my ongoing first author article (desperately waiting for submission) by publishing the draft on Google Docs and adding the coauthors as collaborators, but only one coauthor (a med student) was kind enough to make one little correction this way. The rest is….well the majority of science people are living within the narrow world of Microsoft Office.
Posted in community, IT, Nature, open source, peer-review, science, science journals, science publishing, technology | 9 Comments »
Posted by attilacsordas on June 4, 2007
In What Google Universal Search’s first 30 results know about “biotech blog” I wrote: “Everyday web users are strongly adapted to a situation in which 99% of their information comes from the first 30 results of a Google Search (the first 3 pages with divine power, if the setting is 10 results/page)”
But I was ignorant about (I am truly not a SEO expert) that in many cases, users’ tolerance is restricted to the first 3 results only, says Udi Manber, who oversees Google’s entire search-quality group in a recent New York Times article on Google Keeps Tweaking Its Search Engine: “Expectations are higher now, when search first started, if you searched for something and you found it, it was a miracle. Now, if you don’t get exactly what you want in the first three results, something is wrong.”
I guess that this search tolerance limit strongly depends on the search subject: the “first 3 results” expectation is valid in case of everyday commercial, superficial and basic data searches (who is Malcolm Gladwell?) while the first 30 results rules when the search is about something more context-dependent (why Malcolm Gladwell is an influential guy?) so the search engine faces “higher” user expectations.
(Maybe this first 3 or 30 results opposition is simply not a fruitful one as people are using special search engines, Google services concerning special topics, like scholarly literature, or blog posts. But the intention behind Google Universal Search is to handle all conceivable searches in one unified searching surface. I think it’s time to ask a search expert or consult with my wife as this question is not one that could be managed with 1 search and the first 30 results.)
Update: Anna says: instead of superficial vs. context-dependent, what I am really thinking about here is data vs. argumentation focused search.
Posted in google, IT, Search Engine, technology | Comments Off
Posted by attilacsordas on June 3, 2007
Posted in Aubrey de Grey, Bay Area, california, google, IT, IT&BT, life extension, longevity, presentation, SENS, UK, USA, video | Comments Off
Posted by attilacsordas on May 3, 2007
Maxine Clarke, Nature’s blogactive and web-oriented Publishing Executive Editor blogged on
has an interesting and opinionated editorial on Share your lab notes in Nature 447, 1-2 (3 May 2007). also available at Nautilus.
Her The line of argument is: The use of electronic laboratory notebooks should be supported by all concerned since they “contain data that flow automatically from lab instruments and can be read by all lab members”. This availability to other collaborators should compel the keeping of better records. Most importantly: “If each notebook is allocated a unique identifying code — a permanent alphanumeric string containing information about provenance, creation dates and digital location — it can be cited in journals as a confirmation that the data are safely stored, ultimately available and sharable (with due regard for the rights of the researchers involved). It also confirms that the original data can be retrieved in the case of errors or accusations of fraud.” This way, Clarke the editorial goes on, both “the rigour and transparency of publicly funded research will be improved”.
she the author of the editorial is absolutely right. But there are many, geographically distant interlab collaborations too, not just intralab projects in the vicinity of 2 rooms on the same floor. Let’s put these ideas into context to see them live.
I’d like to step further a little bit as
Clarke the author of the editorial misses to consider the current technological situation: all these nice aims, the standardization (unique URL to every lab notebook), the universal, collaborative sharing of digital notebooks could obviously be realizable by web-based applications (Google Docs, collaborative wikis) rather than Office-like desktop softwares and restricted local networks.
Or more dynamically: can you imagine individual experiments as blog posts, and a lab notebook as a project blog? After all, every experiment has a principal investigator, and all the other participators could be interpreted as commenters. Or this is not the case (we need a group blog in case when the FACS measurement at the end of my cell culture experiment is implemented and recorded by another scientist), and more democratic wikis are the real solutions? Who knows it yet? But the direction is clear. Webtop apps.
Posted in technology, science, editorial, biology, IT, wiki, IT&BT, protocol, Nature, science hacks, laboratory | 16 Comments »
Posted by attilacsordas on April 6, 2007
Google Desktop Beta search for the Mac is now downloadable, which is a viable alternative to the built-in Spotlight for searching any files on OS X with gmail, web integration. You can reach it from a widget-like app (left) or from the Firefox browser as a tab (right). It made my life easier since I am not adapted well to Finder and Spotlight.
Posted in Apple, geek, google, IT, lifehacks, lifestyle, technology | Comments Off
Posted by attilacsordas on April 2, 2007
Today I visited a presentation of Vint Cerf, whose work in the 70s on the nascent Internet Protocols, like TCP/IP became historical. Mr. Cerf serves as “Vice President and Chief Internet Evangelist” of Google, and he has mainly a brand maintaining and popularizer role. Unfortunately he wasn’t asked about his activity on InterPlaNetary Internet Project but I really liked his slide on the first ever 4 processors interconnected as the initial ARPANET between UCLA, Stanford University of California, Santa Barbara and University of Utah‘s Graphics Department. My question to Mr. Cerf was: What is the biggest scalability problem at Google and at the Internet just right now, out of which he answered the latter, although I haven’t processed it fully yet. Picture: My MacBook shot, when Cerf explains Google Earth‘s user-generated level.
Posted in history, IT, presentation, protocol | Comments Off
Posted by attilacsordas on February 25, 2007
Read this nice and brand conscious weekend off story on Official Google Mac Blog. Scott Knaster, Mac Team Technical Writer at Google organized a trip for a “gang of new Mac fans at Google“ from Mountain View to Apple headquarters, Cupertino. At the Caffe Macs they were eating a Google-like terrific food, but not for free, when suddenly “we noticed a slight disturbance in the room, as if all the air had rushed to a single place, over by the salad bar. As you have probably guessed, it was Apple CEO Steve Jobs, grabbing some lunch with Jonathan Ive, Apple’s industrial design guru. As the two moved across the room, there was no great commotion — after all, this probably happens just about every day at Apple — but our Google group and many other folks stopped eating long enough to follow the two rock stars around the room for awhile.” Sounds like a sitting ovation.
Anyway, it would be good to know the ratio of Mac-Windows-Linux users at Google. Guess what? I think Sergey Brin is using a Mac.
Posted in Apple, Bay Area, california, celebrity, google, IT, off | Comments Off
Posted by attilacsordas on February 12, 2007
23andMe is a biotech focused web startup based in Mountain View, California (yes, the Googleplex neighbourhood) self-defined as “an early stage startup developing tools and producing content to help people make sense of their genetic information. Our goal is to take advantage of new genotyping technologies and help consumers explore their genetics, informed by cutting edge science. Genome deciphering technologies have reached affordable levels, allowing consumer access. For the individual, such information will provide personal insight into ancestry, genealogy and health. For society, the collection of genotypic and phenotypic information on a large scale will provide scientists with novel avenues for research.”
Briefly, they are concentrating on the enormous genomics data we already have to analyze them for customers. They are probably right, because in biotech, genomics could be the first field that has enough results, easy measurement methods (a little blood or biopsies), infotech background and enough commercial demand to make the business profitable within 1-2 years. Unfortunately, regenerative medicine and the stem cells frontier are not in this position yet. The next business step could be monetizing data from proteomics, transcriptomics. With the promising combination of computer science, biology and informatics 23andMe is an early bird of a biotech-based web domain, because there will be times when all your genes, RNAs, peptides (and in my opinion: cells and tissues) will be taken into account by your initiative to know your future prospects, and a web-based service is a proper choice for managing all of your biodata. Security problems will emerge, of course.
Read the rest of this entry »
Posted in Bay Area, bioinformatics, biotechnology, business, california, DNA, google, industry, IT, IT&BT, medicine, USA | 5 Comments »
Posted by attilacsordas on February 10, 2007
Check out Grailsearch.org, which was started at the end of January and is hosted by software engineer Jim Craig with a deep interest in aging and bioinformatics. Grailsearch is a “community web portal intended for use by biogerontologists, students of biogerontology, software engineers, biochemists or anyone else interested in working towards the search for systems solutions to the diseases of aging.” Jim was interviewed at Pimm in November, 2006, and said that: “I have adopted life extension as a hobby. I now study microbiology, proteomics and molecular design about 20 hours per week and plan to guide the next 20-40 years of my career through bioinformatics and eventually into de novo drug design with an emphasis on aging solutions.”
The initial set of blog posts on the site seems really exciting for the multi-disciplined systems biologists of the future. As my point of view on indefinite life extension technology is systemic regenerative medicine, I am strongly committed to all the computational based large scale model approaches and quantitative aspects of the human body on which I had an interesting correspondence with Jim last year.
With Grailsearch the geeky IT side of aging research and life extension has at last got a quality representative on the web!
Posted in aging, anti-aging, bioinformatics, biology, blog, IT, IT&BT, life extension, longevity, partial immortalization, pimm, science, science blogs, technology, USA | 2 Comments »
Posted by attilacsordas on January 30, 2007
How many people out of you, life scientists, are regularly updating their PubMed searches through RSS feeds? According to the Read/Write Read Blog 2006 Web Technology Trends “While 2006 can’t be seen as the breakthrough year for RSS in the mainstream, we will probably see RSS bloom in 2007″. It’s January, 2007, so let’s upgrade a little bit.
PubMed is despite all its problems and oldschoolness is the major information source of peer review articles in the field of life sciences. You can make it a little more fresher if you create and save your PubMed searches as RSS feeds. With that users can retrieve new items of their saved PubMed searches since the last time they were connected to their RSS reader. There are numerous RSS readers to choose from, many available for free: Google Reader, NetNewsWire Lite, even web browsers, like Safari, Firefox have built-in readers. Here is the text&screenshot tale of how to activate this useful option:
1. Run a search in PubMed. Say you’re hungry for the novel articles and reviews to the search term “skeletal muscle stem cells” (as I am now), because you are writing an article draft.
2. Choose RSS Feed from the Send to pull-down menu in order to create a feed for that concrete search.
Read the rest of this entry »
Posted in technology, IT, peer-review, lifehacks, science hacks | 9 Comments »
Posted by attilacsordas on January 29, 2007
The Best of Technology Writing 2007 will be published by digitalculturebooks with the guest editor Steven Levy. So they are “asking readers to nominate their favorite tech-oriented articles, essays, and blog posts from 2006. The competition is open to any and every technology topic–biotech, information technology, gadgetry, tech policy, Silicon Valley, and software engineering are all fair game.” I strongly encourage every biotech supporter to choose one and nominate! Although the biotech blogosphere is not too strong yet, there are interesting pieces in it.
Ideal candidates will: Read the rest of this entry »
Posted in biotechnology, IT, IT&BT, open source, technology, USA | Comments Off
Posted by attilacsordas on January 14, 2007
There was a nifty product introduced in this week’s Macworld at Frisco: the Pen-it® NOTES. It is a digital pen that converts hand-written analogue information created using “pen and paper” into digital data, enabling the data to be utilised in various applications. When you used the pen on a special patterned and dotted notebook, the pen transfers the information via Bluetooth to the Mac in vector data form for further editing. I am looking forward to a world where lab protocols and records are instantly made digitally with an application like Pen-it. For that a bigger protocol format (A-4 not A-5) is needed.
Link via MacBreak.
Posted in Apple, gadget, IT, protocol | Comments Off
Posted by attilacsordas on December 6, 2006
Check out the brand new BioMed Search, it is fantastic, currently over 1 million images have been indexed from peer-review journals in biomedical fields and more is on its way. BioMed Search has been created by Alex Ksikes, currently a Ph.D. candidate in Computer Science with focus in Computational Learning Theory at the University of Cambridge (good town, good to be here). The About says: “The goal of BioMed search is to organize figures, images or schema found in biomedical articles. BioMed Search indexes image captions along with the citations to these images. “ Pictures can be seen with full and thumbnail view. Recent Searches, my favourite, show terms recently searched for, with which you can catch research trends. If the number of users grew exponentially, a digg-like real-time spy could spectacularly dinamise the site.
With BioMed Search you can search for general terms like mitochondria, phrases like “proteomics”, search in the title of the articles only for “Mfn1″, get images from an article with a concrete PMID (PubMed Identifier), find images authored by “Nicholls”, limit results to content from a specific year date:1996 (actually just from 1996 presently), and limit search to a specific journal. And this is just by default.
Young science people with an entrepreneurial spirit full of diy hacker skills backed by current web technologies, like Alex Ksikes, who is a real coder, and Moshe Pritsker, biologist, founder of Journal of Visualized Experiments make filtered academic information instantly and easily accessible. And so academic scholar science becomes not just updated, but simply …cool.
via Google Blogoscoped, thanks Anna for the terrific tip.
Thanks Alex Ksikes to make this happen.
Posted in biodiy, bioinformatics, biotechnology, Cambridge, diy, image, IT, IT&BT, open source, open-access, peer-review, science, science journals, technology | 6 Comments »
Posted by attilacsordas on November 26, 2006
And now for something completely different! Sometimes life is just simply life for me without any extension. This is Life.exe. So at the weekends during the largely dead webtimes, I’ll blog about other things than stem cells, regenerative medicine, maximum life extension and biotech. This week offstory is a report, which shows the transformation of the now mainstream, once countercultural Rolling Stone magazine into a Wired-type Zeitgeist patterned techweb conglomerate. I bought the 16th November issue because it seemed like a Wired magazine by cover and content too: (inversely, look at the december Wired cover: it is Rolling Stone-like):
- coverboys and story are not the usual nice bodymaniac popceleb men&women but Colbert&Stewart
- blogs of musicians,
- long report on a radical idea by a planetary engineer to stop global warming,
- a big article with the title: The Baby Billionaires of Silicon Valley.
That is about the Valley Brats, the hidden power clique of under 30 übergeeks in the Bay Area, like Firefox main creator Blake Ross, Read the rest of this entry »
Posted in Bay Area, blog, business, california, career, celebrity, culture, industry, IT, journalism, lingo, media, off, Silicon Valley, technology, US, USA, venture capital | 2 Comments »
Posted by attilacsordas on November 19, 2006
Last Sunday I was in London with my girlfriend and we saw this on a Bloomsbury Book Fair:
Posted in blog, IT, lifestyle, photo, technology, UK | Comments Off
Posted by attilacsordas on November 15, 2006
Kevin Dewalt is an American technology professional, presently working at a VC. Kevin is a strong life extension supporter. We’ve met online at Baris Karadogan’s blog. I specially liked his “happy argument” for maximum life extension on the psychological level, see answer 3.
1. What is the story of your life extension commitment?
When I was 23 I discovered a book called “Optimum Sports Nutrition” by Dr. Michael Colgan. In it he presents arguments for lifestyle and nutrition changes that athletes could make to improve performance. The idea that changing my exercise, eating, or lifestyle habits could change my physical well being, health and longevity thrilled me and I began my quest. I began researching and learning about dietary supplements. At age 25 I became a vegetarian. At 26 I joined the Life Extension Foundation and have followed their recommended supplement scheme since. At 33 I began started a mild Calorie Restrition diet, lost 10 pounds and have remained on the diet. At that time I also began following the writing of Aubrey de Grey (blogterview here), Roy Walford, and others and realized that the only way I was going to be Father Time forever would be through significant advances in science.
2. Is it a commitment for moderate or maximum life extension? Read the rest of this entry »
Posted in aging, anti-aging, Aubrey de Grey, blog, business, career, community, industry, IT, life extension, lifestyle, longevity, Mprize, partial immortalization, US, USA | 4 Comments »
Posted by attilacsordas on November 6, 2006
Briefly: A lot. As you might have noticed, for me as biotechnologist/life extensionist, the most important reference group is the group of IT people, because of the engineering approach, software-hardware tools, intuition concerning technology and funds. After Reason and Chris, our next answerer is Jim Craig, who published his answers here as a comment first by accident. This democracy of comments and reader generated contribution is so welcome. Jim is a lead architect and director of a software team, and the type of IT guy, whose interests can easily be as valuable concerning life extension as biotechnologists, and not exclusively in the long run.
1. What is the story of your life extension commitment?
I have adopted life extension as a hobby. I now study microbiology, proteomics and molecular design about 20 hours per week and plan to guide the next 20-40 years of my career through bioinformatics and eventually into de novo drug design with an emphasis on aging solutions.
2. Is it a commitment for moderate or maximum life extension?
maximum. Read the rest of this entry »
Posted in aging, anti-aging, bioinformatics, blog, community, concept, IT, IT&BT, life extension, longevity, partial immortalization, pimm, technology, US, USA | Comments Off
Posted by attilacsordas on October 22, 2006
Hello everybody, let me introduce myself: I am the first full-time biotechnologist at Google Inc. My job at Google is fascinating: I have to plan and build a comprehensive regenerative database/map of the complete human body which will be the input of the ultimate human regenerative software. It is so, because in the long run, Google Regeneration Clinic will open its doors to offer a continuous regeneration treatment for its patients, aka partial immortalization or pimm. No surprise, that my nickname here at G is: the Pimmer. The aim of regenerative medicine is to regenerate all tissues and organs of the human body with the help of stem cells’ regenerative potential. Theoretically, if all tissues and organs of an adult body were regenerated once, then it could be regenerated two and eventually n times. This technological possibility is called partial immortalization.
Even my bosses do not really understand how the continuous regeneration treatment will work, but they placed their confidence in me. Although not being biotechnologists, they caught the brand-new concept of regenerative medicine, the science and technology built around stem cells’ regenerative capacity: the aim here is to facilitate and amplify or simply replace the native regenerative potential of the organism, the targeted tissue or organ. Regmed does not care about the causes and the detailed effects of the injury, but about the replacement, and the renewal of the damaged function.
So I have the tremendous opportunity to build Google BioLabs and thanks to the cooperation with California Institute of Regenerative Medicine our new experimental lab is about to open. What we need: smart geek biotechers, engineers and 20 years of masturbatory intensity of concentration (the words of Michael Chabon) to fulfill the task. What we already have: the money, the most innovative corporate environment and the lifetime commitment.
Questions for the would-be Google BioLabs members (but I promise there won’t be 7 interviews for 14 hours with 28 Googlers):
1st With an ordinary FACS machine, how long does it take to count 10-100 trillion cells which is the order of magnitude of the human body?
2nd: Delineate a non-invasive method capable of counting so many cells within a day.
3rd Plan the algorithm of the consecutive order of a complete tissue and organ regeneration.
Posted in anti-aging, Bay Area, biotechnology, business, california, concept, google, IT, IT&BT, life extension, partial immortalization, pimm, regenerative medicine, science, Silicon Valley, technology, US, USA | 8 Comments »
Posted by attilacsordas on October 3, 2006
Jason Pontin, editor-in-chief and publisher of MIT’s Technology Review Magazine who was speaking last week, at MIT’s Emerging Technologies Conference had the opinion in a discussion, that “It’s probably fair to say there’s more revolutionary innovation occuring in biotech and in the material sciences (nanotech) than there is in IT at the moment.” Link
It is not by accident that the Magazine is the home of the SENS Challenge aka the De Grey Technology Review Controversy on healthy life extension.
IT folks: more attention please to biotech and regenerative medicine! Thank you.
Posted in Aubrey de Grey, biotechnology, conference, IT, life extension, partial immortalization, regenerative medicine, USA | 2 Comments »
Posted by attilacsordas on September 18, 2006
From SFGate: “Peter A. Thiel, co-founder and former chief executive officer of the online payments system PayPal, announced Saturday he is pledging $3.5 million “to support scientific research into the alleviation and eventual reversal of the debilities caused by aging.”
The grant goes to the Methuselah Foundation a nonprofit volunteer organization founded by Aubrey de Grey, whose SENS is an engineering proposal to fix ageing-related problems and reach indefinite healthy lifespan. Of course, this amount of money is not enough to solve the problem, just compare it to the $3 billion of Proposition 71 for stem cell research funding in California, where the annual limit is $350 million. Proposition 71 provides General Fund loan up to $3 million for Institute’s initial administration/implementation costs. But the $3.5 million comes from one wealthy man, and the 3 billion comes from a very wealthy state.
The grant marks well Bay Area IT entrepreneurs’s and venture capitalists’ growing interest in biotechnology and bioengineering. Take a look at a previous post here: Google’s coming out in biotech: when and why? IT entrepreneurs of Silicon Valley will be the eventual financial engine behind maximum life extension. They’ve got the money and the desire. Would you like to bet? IT money in BT business: sounds like the pattern of the future. Consider Chairman and Chief Executive Officer of Genentech, the most successful biotech company in the U.S., who serves on the corporate boards of Apple Computer and Google. Congratulations for the grant, I hope that valuable experiments will be backed by that. With stem cells too.
Posted in anti-aging, Bay Area, biotechnology, business, california, economics, IT, life extension, Silicon Valley, technology | 1 Comment »