Andrew Su

I initially thought drupal because it's relatively mature. But I like the ideas above. Anyone know of actual deployments of a CMS on GAE/Heroku? - Andrew Su

Rich Apodaca has Chempedia working on Heroku. I suspect that's a custom Rails CMS, but any Rails app should work. Workhabit have a Drupal AMI for EC2 http://www.workhabit.com/labs... - Deepak Singh

For Ruby, there is RadiantCMS, and a newer CMS called Seed that looks promising: http://www.railsinside.com/tools.... Another option would be hosted wordpress.com with custom theme and hostname, although I do not know UCSD's policy on CNAME records that should point to their internal network (although sdcsb.org looks like something they should have no problem with). - delagoya

Don't know about Dreamhost. Choosing a host is always a bit of a minefield. Personally, I use A2 hosting which has been very good. I have built a websites in both Drupal and Wordpress in the past and I would say that if the functionality exists in Wordpress then I would go with that every time. Drupal customization is a nightmare in comparison. It's very flexible, but unless you enjoy... more... - Matt Leifer

Great feedback, thanks guys. Will definitely go check out wordpress for the simplicity factor. Entering the aforementioned minefield, any other hosting recommendations? Seems everyone offers unlimited bandwidth/storage now, the differentiating factors seem pretty slim... - Andrew Su

No, the differentiating factors are *very* large, it is just that you can't tell what they are from the blurb on the hosts own site. For instance, I started out with Servage before switching to A2 because Servage is incredibly bad, but you wouldn't be able to tell the difference by looking at their sites. Unfortunately, it is also very hard to find an unbiased review site that is not... more... - Matt Leifer

At the risk of repeating myself, if wordpress is leading the pack, you should seriously think about hosting it on wordpress.com. For $40 (no ads + domain map) they maintain the servers, apply updates and security patches, etc. The only reason to host it yourself is of course if you need a custom theme, and frankly I host with go-daddy (which is the used-car salesman of hosting) and have never had a problem with their cheapest economy plan. Plus use coupon code WORDPRESS2 for a discount! - delagoya

Ahh, dates back at least to BOSC 2002 from a talk by Jason Stajich http://open-bio.org/bosc200.... I couldn't find it on bioperl.org which is why I thought I was remembering it wrong. But perhaps this has been retired as "official" Bioperl dogma? - Andrew Su

Ah there was formal dogma? I was almost done with Perl by 2002 :) - Deepak Singh

You know, I too was pretty much done learning perl in 2002, but the crazy thing is that my 2002-perl knowledge still allows me to do 90% of what I want to do. Anyway, hopefully Jason will chime in here with the official line... - Andrew Su

It hasn't changed much since 2002. I am pretty sure Jason has the official line. I just liked the basic Perl motto: TIMTOWDI. - Deepak Singh

worse is better - Bosco Ho

Uh Oh. This is going to get ugly - Deepak Singh

Once every ~6 months I convince myself that I should drop perl but every time there is something that needs to be done for yesterday and puff there goes the motivation. Its so hard to change when the transition is a period of veryyyyy annoying inefficiency - Pedro Beltrao

Pretty sure Ewan Birney popularized this; I remember it along the lines of "the first one to code it wins." The idea being that you can discuss object models and the right way to do things all day, but in the end working, easy to use code is what people are going to adopt. I don't remember if there is an official description of the thought process; probably too busy coding. - Brad Chapman

Unfortunately, this hides the idea that code is more than the an algorithm. If you had some clearly written, well documented, simple and well designed code which a new version of blast had broken, and a pile of spaghetti which happened to have been written more recently, perhaps it would make sense to dump the latter and fix the former. You can go too far with perfect design, of course, but you can go too far with macho programming as well. - Phil Lord

I think Ewan was the originator - I think I was just restating the motto. There was some design/developer philosophy in the bioperl.pod that also probably included this. The philosophy is that lots of mailing lists (where our dev is primarily coordinated) are filled with people spouting or complaining about things not being perfect, but in the end working code would win the argument. - Jason Stajich

False choice. Calling it a "service" might be more fitting (it has both a protocol and a data format). - Shiran Pasternak

Shiran, then you would say DAS (service) = HTTP/SOAP (protocol) + XML (format)? - Andrew Su

That's pretty much what all web services are aren't they? REST/SOAP + XML/JSON - Deepak Singh

DAS is a layer on top of these standards. The protocol describes how a client defines object types (e.g., genes) and coordinate slices; The data format describes how the results are represented in XML. - Shiran Pasternak

@Shiron does DAS really defines what is the type of object ? I mean, is "gene" a simple word or is it a component of an ontology ? - Pierre Lindenbaum

@Pierre DAS only defines "feature" as a type. There is no sequence ontology (not last time I looked). But it's up to the provider to define the interface so that a client can request meaningful objects like "genes" (or "pierres," for all it cares). - Shiran Pasternak

thanks - Pierre Lindenbaum

the "preview" button is only fake preview. It takes out the formatting tags but it doesn't show the post how it will end up on the blog. My guess is that it doesn't apply the theme's CSS? Anyway, makes fine-tuning (e.g., picture widths, background colors) rather difficult... - Andrew Su

Ah, OK, you're right, it doesn't apply the CSS style. I write my post with an external editor and I check the style in FF. - Pierre Lindenbaum

I wasn't able to connect yesterday from Rockville, and for the past day, http://downforeveryoneorjustme.com/biogps... reports we're down. But no other users are reporting issues, and we can't reproduce through all other means we have... - Andrew Su

Fine here. UK, 1643. - Simon Cockell

Paul - I think there is a bit of a deeper issue here that academics expect their authority on a subject to flow from the academy easily into the environment of Wikipedia. Never even occurs us to question whether or how this should happen. Need to realise that we need to earn that authority in a new environment. Which leads to my answer. I don't have the time to do the hard yards to earn... more... - Cameron Neylon

Once, one of my blog post about "the Scope trial" was used as the main source for the French article of wikipedia on the subject. One guy just took my post, somehow rephrased it, completed it a little bit, and referred to my blog as a source. I found that quite interesting, I wrote a blog post about it and on the relationships between wikipedia and science blogs. Then another guy read... more... - Tom Roud

I completely agree with Cameron and Tom. As a scientist, I am simply not willing to invest time in a community where authority has to be established independently of authority in the scientific community, where things I write may be deleted by people who have no authority on the topic in question within the scientific community, and where I in return get no credit or attribution for what I have done. - Lars Juhl Jensen

I contribute a few edits per month at the Wikipedias but many more on Citizendium. Why? Because the latter, although it has other drawbacks, shortens the mileage experts have to go to earn and exercise subject matter authority in such a wiki environment. Speaking of which, it is currently in a transition period in terms of governance (... more... - Daniel Mietchen

Pretty much what everyone else said. Wikipedia is thoroughly confused when it comes to authority -- they accept sources they should not and refuse sources they should welcome. I like and use wikipedia but (although I have done a couple of small edits and will continue to add things that don't cost me a lot of work), it's just not worth my time to wade through their editorial policies until those policies are at least internally consistent. - Bill Hooker

I have a short list of articles that I intend to work on or add, but haven't acted much yet - the bureaucracy scares me off. Like others, I make minor edits, but have never found the time to wade through all the documentation such that I would be confident in submitting a large piece of original work. I would actually like to do some sort of two day course (or have some mentorship) in... more... - Andrew Perry

NCBI eUtils are very interesting, recently started looking at them in detail - Mike Chelen

Structured data behind gene wikis sound quite interesting. I haven't worked with APIs and eUtils so far, but there would be several ways to pipe them in R.. - Salvatore Loguercio

Salvatore, my guess is that R would be a pretty difficult way to do this project (great for statistical computing, not so good for text processing and general scripting). But if you or anyone else who knows R wants to use this project as a productive excuse to learn python/perl/ruby, let me know... (oh, and not sure if you were just guessing with the "structured data" comment, but that's spot on...) - Andrew Su

i am interested . know perl scripting - abuzar hamza

do let me know about the work - abuzar hamza

95 or Me. - Paulo Nuin

ME, definitely. Best. OS. Ever. - Chris Lasher

Go on, give Ubuntu a go. - Neil Saunders

2nd the Ubuntu recommendation ;) - Mitchell McKenna

thanks for the thoughts. (Well, except for the snarky ME thoughts... ;) ) Ubuntu maybe as a VM. I'm in the corporate world, and playing nice with the rest of the infrastructure is important. - Andrew Su

I have very, very few interoperability issues using Ubuntu. OpenOffice handles pretty much every MS Office document. One exception is connecting to Exchange servers (I believe this is improving in Evolution). And if you really must, you can always run Windows software under Wine. - Neil Saunders

were you able to play nice with the corporate infranstructure on a mac? - Mitchell McKenna

I can play nice with the corporate and academic infrastructure with a Mac. I don't waste hours of me time fighting to make Windows bearable and don't waste days trying to configure my video card to make the UI less crappy. Not mentioning fighting with OpenOffice. - Paulo Nuin

@Mitchell, yes, the mac platform is fully supported for me. I just didn't like the OS. Very few things were more efficient (shell scripting) and many things were less efficient (office apps, the lack of an alt key for keyboard shortcuts, exchange). and even with 4GB memory, I found myself fighting apparent memory issues all the time. My Dell XPS 13 with 256GB SSD, 8GB RAM arrived today... - Andrew Su

I'll be running what little Win I need using VirtualBox on my Mac. For reasons I can't go into, I need MS Access for a short time, just until I port over to MySQL. Ick. - Christopher Fields

Windows 7, b/c Vista I think is (unfairly) being euthanized. Also, I heard 7 is having a coming out party, so get your tiara ready! - delagoya

apparently IT wasn't ready to go 7 quite yet. I guess that means I'll just get them to reimage when they do (or maybe VM it)... - Andrew Su

win7 is very similar to vista, with modifications to lower system resource usage. disable aero in vista to achieve something similar - Mike Chelen

Win7 and its not even close. Lots of UI improvements and back end stuff. - John Hogenesch

win 7 (+ubuntu). i'm also going back to win next week, after using a mac for almost 3 years :) never got used to the keyboard layout, also memory issues, FF 3.5 crashes all the time, office 4 mac sucks, no total commander, no picasa, etc, etc - Endre Sebestyen

Are you sure it wans't that you weren't understanding how memory is reported? 0 free memory is the most optimal state. - Rich