Disqus - Latest Comments for Deepak

Re: Who owns your data?

Deepak — Sun, 05 Nov 2006 13:45:57 -0000

I haven't done any work in this area yet, but I would like to comment on this subject. Data privacy is a more general topic, but healthcare adds an additional layer of questions.

My concern is that regulators and lawmakers are not knowledgeable to enact legislation on medical data at this point, e.g. genotyping data and biobanks. There are data generated during clinical trials which should be shared by the community (something the FDA is actively looking at). Patients rights group need to be made aware that data sharing in itself does not violate patients rights. Also, if the data are shared, and in some cases made available in repositories, to whom do any downstream revenues belong?

Re: Isn't it time for the Business Guys to get IT?

Deepak — Fri, 06 Oct 2006 09:55:44 -0000

I am somewhere in the middle on this issue. On the one hand, I do agree with you that "business" types traditionally do not get IT at all, nor do they understand the efficiencies that IT can bring. On the flip side, I have seen too many examples of IT not bringing the kind of efficiencies that are expected. In many cases, it is due to poor execution or badly managed expectations, but, it does tend to leave a black mark.

If an organization makes an investment in IT, I believe it is imperative that everyone across the organization understands the implications and advantages. Brown bags are always a good way to do that.

Re: Contact Me

Deepak — Thu, 18 Jan 2007 01:33:15 -0000

Shahid

As translational medicine begins to start making inroads ands and various PGx/Dx approaches make their way into the clinic, one of the challenges I see is the disconnect between bioinformatics/BioIT (my world) and medical informatics/HealthcareIT (your world). I would love to hear your perspective on these issues/challenges.

Re: Contact Me

Deepak — Sun, 14 Jan 2007 19:03:03 -0000

Hi Shahid

Recently I made the transition from a role focused mostly on informatics for discovery to one where a large portion of my time is spent looking at more downstream applications (medical/clinical informatics). Your blog has really helped me understand some of the challenges that exist in healthcare systems, some of are not quite that obvious to me.

Re: Sethi: Everyone is to blame except me

Deepak — Thu, 13 Dec 2007 23:49:05 -0000

Talk about not taking responsibility. I don't know who is to blame and don't really care, but that was a complete copout

Re: The role of academia

Deepak — Mon, 17 Apr 2006 15:25:52 -0000

Hari,

Very valid point, and one I did not address at all. The real picture is a little murkier though. Universities have a lot of very interesting technology transfer policies, and very often the person developing the technology gets screwed (especially grad students and post docs), since the technology belongs to the University and not necessarily the person who developed it. Companies routinely license a lot of technology. That meant a university and usually the inventor getting a bunch of royalties or related fees. What makes the current system more interesting is that in the past the academic would continue with academia and not pay attention to the commercialization. Nowadays, the same academic is more than likely to take that technology forward himself/herself by starting a company, usually with the academic as a CSO or member of the board. That means that individuals are benefiting increasing (commercially) from work that is often publicly funded.

As you suggest, in an ideal world, the startup should support public science. The problem is that most startups don't make money for a while, which makes give back difficult (although many do fund postdocs). My problem is with labs that are run as defacto R&D; facilities for some startups.

The question is this. Should the public have unfettered access to technology/science developed as the result of public funding? Or can some healthy balance be found between public access and the rights of an individual or institution to protects their iP?

Re: Mugshots at Red Hat

Deepak — Thu, 01 Jun 2006 15:06:30 -0000

I missed that :). Hopefully it won't be too long of a wait and it will not become a debate on evolution. Sometimes I feel that is the only scientific topic many bloggers are interested in.

Re: Is it enough to study individual molecules?

Deepak — Thu, 01 Jun 2006 19:35:02 -0000

Thanks for sending this my way. Sean is quite right, and I think some of what he talks about is implicit in being able to work in teams. Teamwork is not about over-specialization, and one could argue that a specialist is significantly hindering his/her own chances to succeed as a scientist. That said, one person can't become excellent at everything. The key is being really good at a subset of areas and having a general awareness of adjacent areas. That should result in efficient teams as well, as opposed to the silo-ed ones that specialization can lead to.

Re: Peer Review: Nature takes the lead

Deepak — Wed, 07 Jun 2006 13:19:41 -0000

Yes, that was my first reaction as well and to a degree I agree. I don't trust the wisdom of crowds. Digg.com is an excellent example. Some of the highly Dugg stories are not of the best quality, and often rather trivial. Let's see. I would like to keep an open mind and there could be mechanisms to police the debates. One thing is for certain. Mandatory data submission will not work if you want industry to publish. But a middle ground, voluntary data submission a certain required amount of transparency is necessary. The ELN part will come about in a bit, but I think the re will be such disparity in ELN access that this might be a problem. However, with appropriate microformats, guidelines and if the scientific community is willing, I think the process can be improved significantly.

Re: The problem is the software - Jack Dongarra

Deepak — Tue, 27 Jun 2006 20:43:52 -0000

I think the problem with grids is that in some areas they have been presented as having this huge ROI and ability to get teraflop computing from loosely networked commodity machines. They have a place, and I might be a little more negative towards them than I usually get towards useful technology, but part of the reason is that in my industry, grids have been oversold, so it has become a bit of a mantra to try and lower expectations.

On the multicore question, we were discussing this at work today. How does one license software on multicore machines? Lets say I have a dual core machine. To me, that is just a single CPU machine with a different architecture, while others argue that a dual core should be treated just like a 2 CPU box.

Re: The problem is the software - Jack Dongarra

Deepak — Wed, 28 Jun 2006 09:44:24 -0000

Unfortunately none of the technical documents I have seen list that, other than saying that they did some heat simulations and that it runs cooler than one might think. I can probably ask someone.

CoComment works only with some blog types. I have used it in blogs that don't appear to have put anything in the comments file, so I am not sure if that observation is right.

Re: The problem is the software - Jack Dongarra

Deepak — Wed, 28 Jun 2006 09:48:13 -0000

Dan

I completely agree about the purchasing decision behind grids. In my experience, if the project is data intensive, a grid can be really useful, especially if the task is recurring, e.g. a team that needs to crunch the human genome every two months or something like that.

Re: The CIO in a life science company?

Deepak — Thu, 06 Jul 2006 15:08:54 -0000

Enough of a tangent to prompt a fresh post.

As you can see I disagree. Not completely, but I do. When I say the CIO's role has to change, I agree that an IT guru is not necessarily the right person. That said, I don't think an academic is either. In my experience, companies run by academics often do not succeed, for many reasons. One being that the right decision might be to adopt technology different from what the academic has championed, but is the correct direction at the time. That is a hard decision for many academics to take.

You need someone who understands science, markets, business processes .. a challenging role to play. Which is why you need someone with the right team in place, because it is almost impossible for anyone to understand everything. You need someone fundamentally smart, capable of objective reasoning, and an understanding of market pressures. You can innovate, but its not done in a vacuum, and innovation takes many shapes and forms as well. The good CIO, IMHO, is one, who recognizes that innovation drives a business forward and adopts the right mix for that particular company.

Note of warning .. industry does not have unlimited resources. In many cases, the resources available might be less than what many academics (especially superstars) have access to.

Re: Life without a laptop?

Deepak — Fri, 14 Jul 2006 19:45:23 -0000

Indeed ... hopefully you made the deadline. I do have some good news. One of those companies that specializes in disk recovery believes it can help, so I have my fingers crossed.

Re: Bio::Blogs carnival

Deepak — Fri, 14 Jul 2006 19:47:28 -0000

I shall keep my eyes (or should I say my RSS aggregator) open

Re: Protein simulation: At a crossroads

Deepak — Sun, 23 Jul 2006 18:39:00 -0000

Oops ... corrected!!! One of the negatives of writing posts in html mode without a spellchecker.

As to the subject itself ... based on what I have seen happening over the past few years, I think scientists have reached the limits of the kinds of computations they can do with current commodity hardware. My concern is that while we wait for the next quantum leap in computing performance, there are options available today that we are not really utilizing to get real answers to real problems.

Thanks for reading!!!!

Re: Protein simulation: At a crossroads

Deepak — Sun, 23 Jul 2006 19:14:30 -0000

I don't have enough of a life to be away from my computer for too long on the weekends.

Protein folding is one aspect, and the problems there are beyond just computer power. The physics of protein folding is an unsolved problem. The current potentials and descriptions that we are using for folding are not correct, although a lot of good work has been done in the past decade (especially the late 90's).

The part that does not need special compute power is genomic-scale comparative modeling. It's not too hard, given enough structural coverage, to run threading or homology modeling programs to predict the structure of proteins from their primary sequence. I think there too algorithms for sidechain and loop modeling can be improved (as well as alignment). The CASP "competition" has shown that there has not been enough improvement over the past 4-5 years.

In general, one needs to develop algorithms that fit current computing capabilities. IMHO, with current commodity hardware, we are close to doing the best we can. To take the next step, we should be using new hardware architectures that allow us to write software differently or solve problems in a different way. Most FPGA type work that I have read about focuses on new ways to run BLAST. Useful, but only a small piece of what the community should be doing.

Re: Things I noticed - La édition première

Deepak — Sat, 05 Aug 2006 21:25:35 -0000

Good question. Actually I used to be more eclectic, but I ended up deleting a lot of posts that fell outside my biotechnology/informatics/business boundaries. For me "relevant" is something that may have an impact on the biotech/pharma industries, especially pertaining to bioIT and computation. Actually, I think this calls for another post.

Re: About this blog

Deepak — Thu, 10 Aug 2006 20:20:58 -0000

I should. It's been a while since I wrote on that. Actually I heard a great talk today which might just give me the inspiration to write something.

Re: Things I noticed - Part Deux

Deepak — Sun, 13 Aug 2006 13:06:05 -0000

I admit that while I understand the informatics side very well, I don't know everything about the capabilities and developments in AI. That said, I have read enough about what Ray has said in the past and completely disagree. Your statement about "smarter than human AI" is an example of people underestimating the complexity and nature of human biology. I don't think that the kind of understanding required is going to happen in the timeframe that many futurists think it will. I have still seen no evidence of the kinds of breakthroughs required. The day will come when we will be able to regenerate tissue, monitor and treat disease in very early stages, but those are still incremental steps in the development of technology.

The other point, one I dont make emphatically enough, is that I would rather see some of the smartest people in the world focus on eradicating malaria, TB, AIDS, that trying to make those in the western world live longer, but that's a philosophical discussion, not a scientific one.

Re: Structure prediction has a long way to go - The PDB says “no” to computational models

Deepak — Thu, 31 Aug 2006 11:01:50 -0000

Strictly speaking even a crystal structure is a model, since it fits the structure to experimentally observations, i.e. the electron density. .. and therein lies the problem. Take space travel for instance. All the calculations that figure out how we get to the moon, go around, it, etc are all "models", but the underlying physics is very well defined. When it gets down to molecular level detail, life gets a lot more complicated. We are some way away from theory that can describe molecular systems the size of proteins at the desired level of accuracy.

Re: Bio::Blogs #3

Deepak — Wed, 06 Sep 2006 00:01:25 -0000

Paras

I don't think I got any entry from you and your blog slipped through my radar. Sorry about that. Please submit an entry for Bio:Blogs #4 which Sandra Porter will be hosting.

Re: The onslaught against scientific publication

Deepak — Thu, 21 Sep 2006 21:40:25 -0000

Couldn't agree more. One thing I forgot to stress in my commentary was the fact that web-based publication gives you the added ability of using microformats and other forms of semantic communication. How much better would all our searchengines get if one could search all that meta information.

Re: The onslaught against scientific publication

Deepak — Fri, 22 Sep 2006 11:53:14 -0000

I would take it one step further. This is not the kind of traning left for graduate school, but should be part of a students training right from the get go (undergrad or earlier). After all, when science advances we retrain ourselves. As someone said somewhere, this is not sexy science, in the long run "knowledge management" is as much a part of 21st century science as anything else. If we fail to do something about it, then we are only hampering our own efforts.

Let's take something very simple. I have a whole bunch of PDFs. I organize them somewhat in folders etc, but when I want to search for a specific term, I don't open every file, but rather run google desktop to find appropriate search terms. Now this is crude, but if microformats and metadata were supported, it would make life even more easier. Everyone knows how to use google (to some extent). The same for Pubmed. Why not empower that mode of search and exchange. The bioinformatics community is at the early adopter part of the curve, so I don't see why the community cannot create the framework and tools that might one day become ubiquitous.

Re: The onslaught against scientific publication

Deepak — Fri, 22 Sep 2006 22:56:38 -0000

Strangely enough, so is Microsoft. They are actively thinking about adding scientific semantics into the Office products.

Re: Things I noticed #8

Deepak — Sun, 08 Oct 2006 11:15:22 -0000

I missed Pierre's gadget. Thanks

I love the Amazon projects. So far the idea has been to promote them to small enterprises as you point out. It's the private angle that I found very very interesting. I wonder how far away you and I are from having our Sun Grid Engine or Amazon S3/EC2 accounts.

Unrelated fields is probably a good thing. These IT types get to have all the fun otherwise :).

Re: “Accelerated Computing” - The floodgates

Deepak — Fri, 13 Oct 2006 18:33:14 -0000

Not just video. My 3yr old Athlon used to scream for recording music. Now as computers have become faster, algorithms have become more complex and some can easily bring it to its knees. There are actually DSP cards for effects, but they have some other issues.

Re: Google custom search

Deepak — Wed, 25 Oct 2006 14:29:14 -0000

Hi Rick

As a subscriber to your blog, I have already perused (and bookmarked) your custom search engine :).

I need to integrate mine with my site, but for that I need to move to a different host. Yahoo is just not the place for such customization

Arunn --> Thanks for your comments. Still some work to do. Again, after I move hosts (something I have been putting off for 6 months)

Re: Things I noticed #10

Deepak — Sat, 28 Oct 2006 01:50:10 -0000

Thanks. We've had a good time getting it up and running

Re: I just “protein-ed” him

Deepak — Sat, 28 Oct 2006 20:09:35 -0000

I have heard people talk about the concept, but didn't know that a product was available. Thanks for the information

Re: I just “protein-ed” him

Deepak — Mon, 30 Oct 2006 21:06:20 -0000

Thanks. I am not surprised at the answer. As I said earlier, I like my 15" laptop screen. One reason I asked was the fact that crystallographers were the first people to ask for laptop support for their times at synchotrons.

Re: Biological content: Access and monetization

Deepak — Thu, 02 Nov 2006 11:34:47 -0000

You're point is well taken. However, the reason we are being able to communicate via this blog, and the fact that you could come across it, is that there is a framework which allows you to do so. Information itself should be distributed across the web and certainly not centralized. Nor should anyone need permission to publish. However, to make the kind of access possible that todays web provides requires the development of some standards and vocabularies. It is the latter that is needed, but it can't happen unless some of the key organizations come together to maintain and agree to those standards.

On the issue of monetization, people are already less willing to pay for information itself.

Re: Biological content: Access and monetization

Deepak — Fri, 03 Nov 2006 03:04:14 -0000

I don't quite agree. The framework provided by my blog software and the WWW, i.e. XHTML, CSS, PHP, is what makes this blog possible. The content is mine, but to disseminate and share this content, there is a framework. My argument is not for the content, but a means to allow the content to be indexed and search. I am open to ideas on other ways to do this, but I haven't been able to think of any. To some extent, we seem to be talking semantics here. Perhaps our definition of framework is not the same or something along those lines.

Re: Biological content: Access and monetization

Deepak — Tue, 07 Nov 2006 09:52:13 -0000

I was hoping you'd read this post. I am convinced that the future of data is some form of loose structure, which will allow indexing services and semantic engines to query the web. In addition, giving a service like postgenomic a plug, memes can be tracked more easily and the likes. In fact the latter is an excellent example of why we need some structure in our data (microformats).

Re: Biological content: Access and monetization

Deepak — Wed, 08 Nov 2006 11:56:26 -0000

I read other versions of that article. I presume you are referring to the Tim Berners-Lee led initiative.

We are a long way from maximizing what we can do with loosely distributed networks of information. Google and the likes were just the start. The "search" is only the beginning :)

Re: Biological content: Access and monetization

Deepak — Thu, 09 Nov 2006 20:22:31 -0000

Pedro

Your last sentence should be framed and sent to every life scientist in the world. If we don't do something about it soon, we will only be hurting ourselves.

Re: Things I noticed #13

Deepak — Mon, 13 Nov 2006 22:23:23 -0000

Touché ... yes it would. There is always room for more than one, but I am partial to the work that Stew has done.

Peter, I agree with you. Although I blog about biology, I am a chemist by training. Biology has one advantage. Data and data management have become central to the subject thanks to all the genome efforts. Chemistry is still some way away from that. Hopefully time will change.

Re: Open source science as an innovation model

Deepak — Tue, 21 Nov 2006 08:46:29 -0000

Ah tenure, another wonderful little concept.

You are quite right about Innocentive (plus there is too much involvement by one specific company), but as I said, it is just a step. In this case a step away from the "not invented here" syndrome.

Re: Open source science as an innovation model

Deepak — Wed, 22 Nov 2006 08:45:10 -0000

... and educating. Which is why efforts like yours are so important.

It is good to see so many people talking about it, and not just in academia. Eventually Open Access is an inevitability, at least from this very biased vantage point. Will it lead to more innovative science? We'll see.

Re: Spreading a meme

Deepak — Wed, 22 Nov 2006 23:05:24 -0000

It almost becomes negative, and I think in science, it's almost self defeating. I'll definitely check out the podcast later today. As you've probably noticed, I've been using open publishing/open access a lot more. Time to start talking about "open science" more as well. The key is to make people understand that open science is all about having an open dialogue and about sharing and not just because we need to, but because it actually helps develop the field.

Re: Self assembly: Some happenings in the bbgm verse

Deepak — Sun, 03 Feb 2008 15:20:58 -0000

I am enjoying it already. As for the visual editor, pretty much the first thing I do with any service is turn of the WYSIWYG editor. Markup is so much faster and effective.

The CC and OpenID were key reasons. With exceptions, I am trying to avoid signing on to new services that don't offer support for both.

Re: Toby Segaran joins Freebase

Deepak — Sun, 03 Feb 2008 15:32:44 -0000

Toby

I am still trying to figure out the most effective way. The current thought is to use it as a queryable backend for data from e.g. docking experiments or bioinformatics search results. Essentially as the equivalent of a triple store. Then one could build apps, where the query engine goes straight to a Freebase store.

Re: Toby Segaran joins Freebase

Deepak — Sun, 03 Feb 2008 15:34:54 -0000

Oh ... and thanks for commenting. Didn't even think anyone would notice :)

Re: The history of science using Freebase

Deepak — Sat, 16 Feb 2008 16:39:38 -0000

[viddler_video=37a1cc04]

Re: Engineering Grand Challenges - Engineering better medicines

Deepak — Mon, 18 Feb 2008 23:10:16 -0000

I didn't really pay attention to the essays, since they were pretty "light". I picked out the items they had selected and wrote some stuff on the ones of interest at this end.

Re: Around the Web - Feb 16, 2008

Deepak — Mon, 18 Feb 2008 23:12:38 -0000

Maxine

You're quite welcome :)

Re: Yahoo: Living up to the talk on Hadoop

Deepak — Wed, 20 Feb 2008 19:33:59 -0000

That could be the case, and for some reasons I find the Yahoo properties to be very discombobulated. For whatever reasons, I don't think of Flickr or del.icio.us as Yahoo properties (and in the wake of the Microsoft situation, I really worry). My #1 objection to the Microsoft situation (which I think is going to get done) is that Yahoo is such an open source company.

Re: Ligand docking memories

Deepak — Sat, 01 Mar 2008 02:28:26 -0000

Depends. I was doing QMMM around protein active sites 10 years ago, but in the docking community with an emphasis on throughput, in general docking functions used a soft potential and a mostly rigid receptor with flexible ligands, and scoring functions were rule or knowlede based. As computers have become more powerful and with an emphasis on quality it's become more common to use flexible receptors and higher order potentials. QM is still rare (too slow). As someone once told me, you have to be faster than the medicinal chemists :).

In this case, it was more of a personal win, to get the structure-based drug design folks to start thinking of using MD-based search schemes and MM-based potentials. The above talk probably uses a modification of Charlie Brook's CDOCKER method and a full workflow (conformer generation, etc) in Pipeline Pilot.

Re: Your personal health: Trusera ready for lift off

Deepak — Sat, 01 Mar 2008 11:06:39 -0000

I had heard of dailystrength but not mdjunction. As David Hamilton wrote earlier, there are a ton of Health 2.0 companies. Lots of overlap and in time, I believe things will settle down/consolidate.

Trusera is local to Seattle and I got to hear the backstory when the company was first founded. Plus it has quite the rockstar team behind it. IMO, the ones that will do best are the ones that go with a "less is more" approach. Too many sites just try and do too much. In this case, it's all about personal stories with some expert content. Makes a lot of sense to me. In the end success lies in building enough of a user base for the wisdom of crowds to be relevant and in execution.

Re: Your personal health: Google Health imminent?

Deepak — Sun, 02 Mar 2008 15:25:17 -0000

lol ... too funny

Re: Why I should get a beta for Twine?

Deepak — Sat, 15 Mar 2008 02:11:26 -0000

They're definitely playing it safe. It's got a ways to go in terms of usability. I'll post my own review once I have built up a sufficient network and content.

The way I look at it, look at it as an application that extracts entity information from your content and uses that to build a graph of linked data (under the hood) and serve up recommendations and content based on that. It reminds me of Calais to a degree, but it's meant to be an application and not a service (at least at this point). Will be very interesting to see how it evolves.

Re: Does Microsoft’s HealthVault really protect your privacy?

Deepak — Mon, 15 Oct 2007 13:18:03 -0000

Etienne is spot on. IMO data must be stored server side, but from the consumers perspective that is a huge leap of faith.

Openness is key. However, I do think that there are a lot of policy issues that need to be resolved at this point. HIPAA, etc must be updated and data ownership issues need to be resolved.

There is a value and a business model here, but it will require a lot of education, pin-point execution and the collaboration of a number of parties including the consumer

Re: Does Microsoft’s HealthVault really protect your privacy?

Deepak — Mon, 15 Oct 2007 15:13:23 -0000

I would extend the question a little more. What is the goal of the personalized health record? Is it meant to put the user in complete control (that has its own set of risks)? Is it meant to be a personal guide, providing information, etc to help the informed patient make decisions, while giving them access to data from tests etc.

The latter is far more feasible. You are quite right, the business models are still uncertain. I do think that highly relevant advertising has a place in this space. What kind of returns could you get? I don't know. However, in the end, and perhaps this will help in giving these services value in the minds of the public, the freemium model might be the best one here.

For now, I think the PHR is a bit of a toy, but I do believe that the idea has legs, BUT only in the appropriate environment. To flog a dead horse, ownership standards MUST be established first, as well as rules on advertising, etc.

Re: Life sciences briefing: Monday, Oct. 29, 2007

Deepak — Mon, 29 Oct 2007 13:21:09 -0000

Looking forward to your analysis on the Microsoft acquisition

Re: Will 23andMe and Navigenics lock up your genome and charge you for the key?

Deepak — Tue, 30 Oct 2007 20:33:07 -0000

I suspect that the quoted figure would include not only testing fees, but also sales of kits, reagents, arrays, assays, data management systems etc

Re: Knome turns to China for genome sequencing

Deepak — Fri, 11 Jan 2008 14:22:17 -0000

BGI did announce a services business (probably in anticipation of this announcement) earlier this week, so it looks like their mission statement is changing.

Re: “Drug engineer” Numerate rises from the ashes of Pharmix

Deepak — Tue, 12 Feb 2008 22:24:41 -0000

I don't know anything specifically about Numerate so my answer is generic and not targeted at the company in particular.

It's not quite correct to say that rational drug design has not yielded any drug candidates. Yes it might be hard to pick one drug and say "this exists because of rational design", but on the other hand at pretty much every pharma company computational chemistry/molecular modeling are part of the discovery process.

There are also too many examples of in silico companies trying to become drug companies based on a computational platform. Based on my own experience, that's just not a feasible model. I'd love to be proven wrong, but such companies are likely to find much more success if they functioned as service providers. In an increasingly outsourced/virtual pharma business, my suggestion is that that companies like Numerate would be likely to be much more successful as part of a larger company where there technology provides a competitive advantage, or as a boutique service provider to the pharma industry which is always in the hunt for good molecules.

Re: “Drug engineer” Numerate rises from the ashes of Pharmix

Deepak — Tue, 12 Feb 2008 22:30:24 -0000

Come to think of it, my argument above directly points to Pharmix. Numerate seems to be going to partnership route that I suggested earlier instead of trying to go it alone.

Re: “Drug engineer” Numerate rises from the ashes of Pharmix

Deepak — Wed, 13 Feb 2008 12:58:21 -0000

David

Life everything in this industry, people keep waiting for that magic bullet, but I have yet to see one.

Will be interesting to see where this goes. Investors often lack the patience that is required for a small company to grow into a drug company.

Re: Decloaking 5AM’s stealthy ImmunoNewco — more details

Deepak — Sat, 01 Mar 2008 18:23:11 -0000

Stealth definitely seems to be something from another era (one before Google). Will be interesting to see what transpires here.

Re: Twitter Launches Mobile Interface | Laughing Squid

Deepak — Sat, 05 May 2007 21:36:26 -0000

They need to move the main site over to that look n feel. It's much nicer

Re: Screencasting: Search for the Narrative

Deepak — Sun, 25 Nov 2007 02:22:28 -0000

I was inspired by Beth's screencast as well. I am hardly as creative as you folk, but it will be very interesting to see how I end up using screencasting for material other than demonstrating something. In that sense, I have been using picture-in-picture recently and yes it is quite powerful

Re: 2007/03/11/twitter/

Deepak — Sun, 11 Mar 2007 17:14:55 -0000

I am with Chris. If people start using it as a public chat channel, then I am going to quit. It took a lot for me to adopt Twitter (I am still not sure I get it), but the microblog/broadcast/privacy aspects make some sense.

Re: I’m not a Guy kind of Evangelist

Deepak — Thu, 12 Jan 2006 16:15:37 -0000

I have always fancied myself as some sort of evangelist (for using computing to further the cause of life science), but avoid the term as much as possible, since (a) scientists are not that passionate about the geeky tech stuff, and (b) the percieved religious connotations.

You raise one very important point. It is definitely better to have skeptical, educated customers. They keep you on your toes and make sure you get your facts right and don't "evangelize" blindly.

Re: Looking at Vista

Deepak — Tue, 01 Aug 2006 13:33:41 -0000

I am a marketer and to be honest I think "more features" is an engineering mindset (having been on that end as well). Vista should focus on the correct features, not making it everything for everyone, cause that only fulfils the law of diminishing returns.

I am a Linux user, but the great thing about OSX was that Apple basically tossed out their existing OS model and built something completely new. Vista should not be an upgrade on XP, but something completely and not just a clone of OSX either. The OS world could have used a shot in the arm, which I don't think Vista is going to be. I could be (hope to be) wrong, since I do use windows, but I signs suggest otherwise.

Re: Looking at Vista

Deepak — Tue, 01 Aug 2006 14:10:59 -0000

Robert, but the proof of the pudding lies in the eating, doesn't it. One has to have confidence in the product. If Apple had continued down the path with OS9 etc, then they really would be a purely iPod company. Yes there were people who were mad (I know some of them). The reason so many people are using powerbooks today (apart from the cool factor) is the OS. With the switch to intel, they took another risk (I am not sure its going to pan out, but that's another thread). Microsoft has to take calculated risks (I admit its too late for Vista at this point). If it continues along its current path, as the OS becomes less of a focal point, the user experience will become critical. A few years ago, who would have thought that a number of people at leading biotech or software companies (just to use Google as an example) would be using a Mac at work.

The point is that by taking risks Apple has resurrected itself from the mess it was in around 10 years ago. Microsoft should not rest on the safety net of its market share. Consumers are hoping to see some risk taking and something fresh.

Re: Richard tells me to explain my view on Google Calendar

Deepak — Sat, 19 Aug 2006 11:55:02 -0000

I use Gcal all the time, and its become an integral part of my workflow. I subscribe to a total of 5 calendars, love the look and feel and its just a breeze to use. Sure there are a few features that I wish it had, but it will happen in time. Hopefully it won't get too bloated.

All important reminders are sent to me as text mails, so I don't really miss not having an offline option. I do add an ical subscription from gcal to Mozilla calendar as a backup, but I have not looked at it in at least 2+ months.

Re: Google Writelys home new version of online word processor

Deepak — Sun, 20 Aug 2006 20:33:13 -0000

I would say that I am online, or capable of being online 80-90% of my waking hours. At work I am online all the time. For many tasks, I don't see why I wouldn't use something like writely. I actually do this a bit with writeboards from 37signals. If I have connectivity, I tend to type in notes directly into a writeboard. If not, I use use a text editor and then upload when I am online again. Usually works.

IMO, for collaborative work, Writely and the likes beat offline word processors. While the time hasn't come yet, I can see the Writely's of the world becoming more widely used over the next decade.

Re: Feedless bloggers frustrate

Deepak — Wed, 23 Aug 2006 18:31:51 -0000

Another way to detect feeds is the Google Toolbar. I use it to add feeds to bloglines (I recently switched from Sage when I found I was using different computers).

... and yes, whenever I need to introduce anyone to RSS, I send them to the BBC site. They do such a wonderful job.

Re: Feedless bloggers frustrate

Deepak — Thu, 24 Aug 2006 11:49:58 -0000

And that's somewhat counterintuitive, since feeds are probably more useful in some ways and extend beyond blogs.

I would like to see one development. Feeds that can be filtered. Some sites allow users to set up queries which can then be converted into feeds. I find these most useful. Perhaps RSS 3.0 can include this in the standard?

Re: Where’s Google in the conversation?

Deepak — Thu, 24 Aug 2006 20:27:37 -0000

Another place where Google Earth, e.g. finds good use are these avian flu maps from Declan Butler

Re: Is Akismet down?

Deepak — Sun, 27 Aug 2006 02:44:18 -0000

I have got more spam in the last 5 hours than in all the time I have had my blog, so something is definitely going on with Akismet. What I want to know is how does Akismet work with hosted Wordpress installs (as opposed to Wordpress.com)

Re: Is Akismet down?

Deepak — Sun, 27 Aug 2006 03:34:33 -0000

Well hopefully it is a temporary glitch, since Akismet is the best blogging tool that no one talks about (cause it works so well)

Re: Why I love Automattic

Deepak — Sun, 27 Aug 2006 13:26:21 -0000

No spam in the last hour or so .. fingers crossed

Re: Kathy Sierra is my hero

Deepak — Sun, 08 Oct 2006 11:36:52 -0000

What a wonderful article!!! The one blog I don't miss. Her "featuritis curve" is my desktop background and stuck on my wall that every product manager (especially now that I am not one) and developer gets to see it if they walk into my office.

Re: Another committee takes the "soul" out of Robert Fripp

Deepak — Fri, 10 Nov 2006 11:00:28 -0000

I am officially POed. How can someone take one of the most unique guitar players ever and make him sound mundane? I haven't heard the sounds, so I will reserve judgment, but this sucks

Re: Full text feeds pay off for this blogger

Deepak — Sat, 09 Dec 2006 21:44:50 -0000

Count me in the crowd that dislikes partial feeds. Perhaps more people should offer people both options.

I also get the full feeds for this blog in every feed reader I have used (nowadays Google Reader)

Re: Jeff Sandquist scores one for Microsoft

Deepak — Sat, 09 Dec 2006 21:46:20 -0000

Rory

Can't say I disagree with the analysis. Maybe a raise, a fancier title, but keep him in the same role. That would work.

Re: “Twittering” away the time

Deepak — Wed, 27 Dec 2006 10:41:43 -0000

I still don't get twitter. If I had 10 close friends in town, maybe I would get it. My first reaction was "I'm just too old", but I think Scoble shoots that theory in the foot.

Re: Google Reader behind?

Deepak — Sat, 20 Jan 2007 11:29:33 -0000

I was using both Bloglines and Google reader side by side for a while, since I was familiar with bloglines. I was just so much faster in Reader. NO speed issues here (and I have a lot of feeds). I just don't like the Bloglines user experience as much.

Re: Do A-list bloggers have a responsibility to link to others?

Deepak — Sun, 28 Jan 2007 14:54:24 -0000

Do A-list bloggers have a responsibility to link to others? Not at all. Why should they? I suspect the flip side is more appropriate... while they don't have the responsibility of linking to other bloggers, it is irresponsible of A-listers not to link to other bloggers when they are inspired by something that they read on a smaller blog, even if it is not what they end up writing about.

Re: Jim Gray, one of Microsoft’s smartest, is missing

Deepak — Tue, 30 Jan 2007 12:06:35 -0000

:(

I hope they find him soon. A coupe of months ago, one of his presentations inspired me to write a blog post, and he very graciously gave me permission to use some of his figures.

Re: I removed Snap’s previews from here

Deepak — Wed, 31 Jan 2007 01:18:13 -0000

Phew!!! Thanks

Re: Which blog search engine is covering Demo best?

Deepak — Wed, 31 Jan 2007 23:44:17 -0000

Adding to the unscientific voices, I've noticed a lot more traffic from Google Blogsearch in recent weeks. From roughly a 10:1 ratio in favor of Technorati, recently Google is probably ahead. Most of the traffic from Technorati is from Tags, not search. I am not sure if it is because Google is giving better results, but it definitely catches them faster.

Re: New blog software to watch: habari

Deepak — Mon, 19 Feb 2007 01:08:53 -0000

The developer of my favorite WP fork, K2, is also involved with Habari, so I am looking forward to checking it out.

Re: Google Reader taking the day off?

Deepak — Mon, 19 Feb 2007 13:30:07 -0000

No issues at this end either. Used it quite a bit over the weekend.

Re: Could corporate types use Twitter?

Deepak — Mon, 19 Feb 2007 16:07:27 -0000

The question really should be ... "Should anyone use Twitter?" :)

Re: All for four notes in Windows Vista

Deepak — Sat, 03 Mar 2007 23:39:28 -0000

I also found the historic part funny, but since there is no such thing as "too much Fripp" who cares. For Service Pack 1 they should grab Trey Gunn and record him :)

Re: Celebrity won’t save you

Deepak — Wed, 16 May 2007 01:19:30 -0000

I was quite surprised to find out that this was Guys new project. I don't think it would have received a 50th of the press if guy wasn't involved. I admit I haven't taken a look at it, and don't plan to. It might even be a raging success, but at least for a bit, Guy's light is shining a little less brightly.

Re: If you are going to sell your soul…

Deepak — Sat, 23 Jun 2007 17:32:57 -0000

I am not sure about this being such a big deal. It's not like they wrote big posts praising the hell out of Microsoft. Obviously, they were endorsing the microsoft campaign. Nothing really wrong with that. Should they have disclosed? Probably, but it was rather obvious too wasn't it?

It's all a gray area, and while I am not sure this deserves the attention it's getting, we also need to figure out what the blogger boundaries are, before some real money and ethics issues create the mother of all firestorms.

Re: Why can Leo Laporte and Disney do it, but Mike Arrington and TechCrunch can’t?

Deepak — Sun, 24 Jun 2007 13:20:05 -0000

Looks like we've stumbled upon a very gray area here. I don't see much wrong with the campaign. Even though it was obviously a microsoft campaign, disclosure should have been done up front.

Arrington rubs a lot of people the wrong way. Again I wonder how much this would have been an issue, if Arrington was not involved, and perhaps the campaign had been done by a non-FM company?

I wonder where this will all end up.

Re: Twitter vs. Pownce

Deepak — Thu, 05 Jul 2007 02:51:08 -0000

Twitter is by far the simpler to use and IMO is a better microblogging platform. Pownce is better looking and I find it better to communicate with friends (the sets feature is cool).

Re: Is the A list dead? Is blogging dying?

Deepak — Sun, 08 Jul 2007 22:02:46 -0000

Robert,

I must disagree. Perhaps the reason for the downturn in blogging is that too many people are saying the same thing and not providing enough original insights. Twittering, which I love, can never replace blogging. It could replace the personal blog if the blog is about what you are doing (as billg suggests), but the depth of analysis provided by some of the better blogs out there are not going to be replaced by Twitter, Pownce or Facebook.

Of course, time is limited. Maybe people are spending too much time on Facebook and do not have time to peruse blogs as much as they used to.

Re: The biggest problem for Facebook’s app platform

Deepak — Fri, 13 Jul 2007 01:19:58 -0000

The Jaxtr app seems to work properly, as do the kyte.tv and splashcast apps. Of course the native Facebook apps are just fine. Picnick has worked for me thus far. I would say the Twitter and Pownce apps have been the biggest disappointments, and the last.fm app rocks, but is not yet 100% stable.

Re: Do Pageflakes and Netvibes have any chance against Facebook?

Deepak — Mon, 23 Jul 2007 11:55:01 -0000

I think you are overstating the fact. I love Facebook, but the first page I see every morning is still my iGoogle homepage. I like collecting information, not seeing what my friends are up to. That's part of my life, but aggregating, reviewing and making use of collected information is much more important. I do agree that Facebook is a great portal into my life, but it's not my entry point to the internet. Not yet anyway.

That said, I have no interest in social networking aspects to my personal home page.

Re: Kyte.tv vs. PodTech.net (Adobe announces new Flash player)

Deepak — Tue, 21 Aug 2007 10:14:01 -0000

I am using Kyte.tv to supplement my blogging and online presence. It has the capability of providing very interesting real time feedback and for me to discuss things with a different audience. I definitely find it to be the most effective of all the platforms out there, at least for me. Picked it up after your interview on Podtech and I am glad I did.

Re: Kyte.tv vs. PodTech.net (Adobe announces new Flash player)

Deepak — Tue, 21 Aug 2007 19:38:23 -0000

Lets not forget YouTube, Blip.tv, Splashcast, etc in this discussion. If you want to get a video of your cat out there, and there is no need for interactivity, YouTube is as good a place as any. If you want to get your video podcast distributed, Blip is fabulous. For aggregating content and making it available to others (or just yourself), go Splashcast. UStream and Kyte have been discussed above.

What I find amazing is how quickly video has become part of the personal content distribution. As a particular fan of audio podcasts, I almost feel sorry that podcasting might never really get its day in the sun because video will just become the dominant medium.

Re: Google getting into Facebook territory?

Deepak — Sun, 09 Sep 2007 11:42:16 -0000

India too. There are probably, just a guess based on population, more Orkut users in India than Brazil.

Re: TechMeme list heralds death of blogging?

Deepak — Mon, 01 Oct 2007 18:52:03 -0000

First things first ... Francine is quite right. Tech is not the end all of blogging.

Let's also not forget that there are a lot of people airing out their thoughts on the Facebook's, Twitter's, Vox' etc of the world. I know a lot of people, especially back home in India who are not on Twitter, but are on Vox, cause they can control who gets to see what.

Re: Seesmic vs. Hictu: a lesson in bootstrapping

Deepak — Mon, 08 Oct 2007 16:19:52 -0000

Robert

Do you know how Seesmic compares to Kyte? Not having had a chance to try it yet, the first thing when I saw the description was that this is a marriage of Twitter and Kyte.

Re: Seesmic vs. Hictu: a lesson in bootstrapping

Deepak — Mon, 08 Oct 2007 16:55:21 -0000

It would seem to me that they will clash at some point. Who executes better will win. Seesmic will have to get into those two spaces for long term success.

Re: Some Microsoft balance? HealthVault!

Deepak — Mon, 08 Oct 2007 17:00:55 -0000

I blogged about HealthVault the other day and there was quite and interesting discussion in the personalized medicine blogosphere. Sticking to just the microsoft angle, it almost seemed to me, once I had given the site a try, that in their eagerness to beat Google, they had released a half finished product. I do get the idea of where they want to go, but the implementation leaves much to be desired

As to the specific subject of personalized health records, there are way too many variables right now. Privacy is only one of them. The bigger issue is data ownership and the role of the personal online health record. Is it meant to be a personal guide to healthcare, much like Mint/Quicken would be for financial planning, or the definitive health record accessible by healthcare provider and payer? Who decides who gets to see what information, etc etc. Until some of those questions are resolved, online health records can only remain in the guide category.

I also worry about patients thinking they have sufficient information and making incorrect decisions. Anyway, these are early days.

Re: Some Microsoft balance? HealthVault!

Deepak — Mon, 08 Oct 2007 17:49:32 -0000

Well Aetna has their own PHR blackbox, CareEngine, which explains their attitude to HealthVault. I agree that given a choice between Aetna and MS, I would choose the latter. The models are also different. CareEngine is designed for you to work with Aetna and your healthcare provider to make health decisions, but the secret sauce behind CareEngine's recommendations, at least to the best of my knowledge are just that, a secret sauce. I just don't trust an insurance company in this regard

Re: Kara Swisher is right about Facebook apps (new Kyte.tv player)

Deepak — Thu, 11 Oct 2007 16:52:06 -0000

I am trying to figure out the new look myself. There are some new features that I like, but not sure about the color scheme. But it's early. More after a day or so

Re: The you-don’t-need-more-friends lobby

Deepak — Mon, 15 Oct 2007 00:25:21 -0000

Robert, much as I appreciate your work, I have some disagreement with you on this. First of all, Flickr is not the best example. To upload more than a certain number of pictures a month you have to pay. This rules it out for quite a few people, or they end up improvising of paying.

Second, while it is true there could be scaling issues, you develop software for a market, not a customer. So unless the Facebook market moves towards users with 1000's of contacts, then the limit might not be a bad idea.

That said, if it is a scaling issue, they need to address it, since markets do change.

Re: Twittering Shelley

Deepak — Thu, 15 Nov 2007 18:37:08 -0000

Tom's point above is quite correct by and large, but specifically speaking to Twitter, if anything it is underhyped. Or to put it differently, if there was less "web 2.0" geek marketing speak associated with it, it's a brilliant and very useful service.

Case in point, and this is not the first example, Supercomputing 2007. SC07 is currently going on in Reno and it is hardly your usual web 2.0 fanboy conference. A number of people are tweeting sessions, newly released hardware platforms, key topics from talks and posters, etc. One person even reached out to me (I don't know the person) and asked me if there were specific subjects I was interested in. I am not in Reno (in Seattle), but I have a decent idea of what's going on.

At every conference I have attended this year (of which only one would qualify as a web 2.0 one), I have used twitter to communicate with others there and with people interested but not there. It's difficult to beat that.

Re: The brand promise of Apple

Deepak — Sat, 17 Nov 2007 16:01:07 -0000

Lets get all disclaimers aside. I've used all possible OS' and systems (even VAX), and personally consider myself a Linux fanboy. I have every major OS represented in my house.

IMHO OSX is the best desktop OS, and Macbook Pro is a beautifully designed machine. However, Apple, for whatever reason seems to get a free ride on all kinds of issues, partly due to its marketing machine. Whether it be not including Java, or funky hardware issues, or the lockdown of their products, they get a free pass on issues for which they would be skewered if they were any other company.

Re: The serverless Internet company

Deepak — Sun, 18 Nov 2007 18:35:56 -0000

Bioscreencast is also moving to EC2/S3. We have a hosted server that we use for development/staging, but all screencasts will be served up from S3 and we have other plans as well, especially for EC2.

As people above have noted, not having inhouse servers is nothing new. It's the flexible capacity and utility aspects of Amazon, 3Tera, etc that are so cool and novel, at least for running businesses.

Re: Where the hell is Mark Zuckerberg and Facebook?

Deepak — Tue, 04 Dec 2007 09:35:30 -0000

I agree with Bob. This whole situation shows a lack of foresight and management experience. Personally I don't have as many issues with Beacon as others, but a seasoned manager would have probably thought through the scenarios and handled any negative fallout a lot better. Mark is still a kid. Sergey and Larry were smart enough to bring in a CEO, Zuckerberg needs to do the same, otherwise there will be other missteps, a lot more really.

Re: Where the hell is Mark Zuckerberg and Facebook?

Deepak — Tue, 04 Dec 2007 13:42:57 -0000

Jeremy ... lol .. so true

Re: Dopplr: cool online service for frequent business travelers

Deepak — Sun, 16 Dec 2007 01:21:01 -0000

I've been on Dopplr for a while and it's been useful, especially to keep track of people who show up at some of the same conferences.

That said, I am torn between Dopplr and TripIt. For now I am using both. I really like TripIt's functionality, but have more connections on Dopplr.

Re: Steal my content please, Part II

Deepak — Thu, 20 Dec 2007 15:56:43 -0000

I think the problem lies with the content producers as well (although users need to understand CC, etc). Lane could have chosen a service more conducive for professional photographers, e.g. Smugmug. If you're that touchy about it, use the right safeguards.

Re: Why are some bloggers turning on Apple?

Deepak — Tue, 25 Dec 2007 13:03:11 -0000

The thing is, Apple is doing what it's always done, except that people are beginning to notice, since their volume and mind share has gone up. For years, I never owned an Apple product due to their closed/proprietary policies (hey I am a Linux guy). Strange thing is, that in a couple of weeks I am selling my desktop PC and buying a mac to complement my Linux box. Fact remains that with Parallels/VMWare, I can enjoy the best of both worlds and for what I a doing these days, a Mac makes more sense. I figure that if I am going to deal with hardware issues, I'd rather do it with a computer that looks cool and has an OS I like (I have never, ever liked Windows, but have learnt to tolerate it)

Re: Google Reader needs GPC

Deepak — Wed, 26 Dec 2007 13:51:32 -0000

Non-story. When you have a public RSS feed and can turn of people whose feeds you don't want, I just don't understand why people are getting upset about it. It's a little exasperating actually. We want our shared items to be tracked on friendfeed, put up widgets, etc. There are other options for private sharing. Google could add that feature, but that's not the current intention and it was pretty obvious from day #1

Re: Why we’re going to FastCompany.tv

Deepak — Wed, 16 Jan 2008 12:42:04 -0000

Argh ... one more video network to keep an eye on.

Just kidding of course. Congrats and good luck.

Re: Hope

Deepak — Sat, 19 Apr 2008 12:13:36 -0000

Moments like these are the ones that put our often silly tech world arguments and disputes into perspective.

Re: Platforms Are The New Portals

Deepak — Sun, 10 Dec 2006 14:22:35 -0000

It is all about what I call custom portals. An example is my personalized google page. That is my portal to the internet now. It's where I can see my latest emails, latest feeds, news items, follow my stock porfolio, flickr tags, youtube, even my weight, etc etc.

I wonder where a service like Pluggd, which I really like fits into this discussion?