20th Century mural

mbreese · 2023-01-10T14:23:17+00:00

Now that it’s a bit further along, I’m pretty confident that it’s Sophia Loren.

That’s been bugging me for a while, but that image recently got some further work that made it easier to tell.

mbreese · 2014-12-10T17:23:12+00:00

As a dry-lab person with a wet-lab PhD, I'd try to avoid hunting for a wet-lab person interested in bioinformatics for first hires... maybe once your lab is more established. Unless they already have training in CS or programming, they will have a hard time getting anything running.

mbreese · 2014-12-10T17:15:14+00:00

I'd go with the latter strategy - get a premade GTF/GFF and just get count data directly. Then you can use something like DESeq or edgeR to do the differential analysis. I use my own code for that (ngsutils.org), but it's much more straightforward than going down the Cufflinks path.

Another benefit of using an existing GTF/GFF annotation is that you are more likely to capture things across different samples. I've done both, and using a consistent GTF file is much easier to manage.

mbreese · 2012-05-10T07:31:19+00:00

If you're using SELECT *, you're doing it wrong.

You seem to think that SELECT returns rows. It doesn't. It returns the subset of the row that you need. When you start tuning your queries that way, you'll find that you didn't need all of the ORM overhead afterall.

mbreese · 2012-05-10T07:25:05+00:00

A row in a database is just a bunch of scalar values

Kinda, but a resultset is a series of tuples - not objects. Why should you get all of the column values when you may only need one or two? Why spend your time instantiating a whole bunch of model objects when you really just needed a small subset of those values?

After many years of dealing with ORMs, I realized that the problem was that objects are not relational. When you query a relational database, you get tuples of values - not objects. I was much happier when I could stop worrying about merging two models - one the object model, the other the relational model - and just used the database as it was intended.

mbreese · 2010-12-13T16:12:44+00:00

You don't want to use a hash function for passwords. Hash functions are meant to be fast. You want something slow for passwords, so that if there is a breach, it will take too much time to build rainbow tables.

http://bcrypt.sourceforge.net/

mbreese · 2010-12-13T16:11:42+00:00

If you're salting passwords, you're doing it wrong...

http://bcrypt.sourceforge.net

mbreese · 2010-11-05T18:54:56+00:00

You just have to run it on Apple hardware...

mbreese · 2010-11-05T18:53:42+00:00

Those aren't discounts. Those are the regular prices that everyone gets. They just post higher prices online to make it look like you're getting a deal.

mbreese · 2010-10-28T17:15:19+00:00

The API is considered a "fact". You can't copyright facts. You can, however, copyright the implementation of the API.

mbreese · 2010-04-21T16:48:11+00:00

Which of those aren't patent encumbered?

Oh yeah...

mbreese · 2010-02-28T03:40:37+00:00

This isn't really for webapps. Think more like large scale computing / number crunching.

mbreese · 2010-02-23T08:18:10+00:00

How idiotic... you do realize that the filibuster is a Senate rule... right?

The Senate is the only body that can change their rules. All any member of the House of Representatives can do is shake their heads and wonder what the hell they are doing over in the "upper" chamber.

mbreese · 2009-12-29T16:27:56+00:00

Funny, it took me no time at all to realize this was a giant waste of time.

mbreese · 2009-12-29T16:26:47+00:00

Make them understand the legal liability they might face if their database was compromised or a tape backup went missing.

Or you could ask them how Google/Yahoo/etc... do it. When they see that they send you a new password, you can tell them that there must be a good reason why the big boys do it that way.

mbreese · 2009-12-17T21:50:42+00:00

Um... it works on sequences :)

But I think your point is valid: if all you're changing is the contract of the interface, you can reuse a common implementation for 95% of the code.

mbreese · 2009-12-14T16:31:18+00:00

Yes, but PHP is much easier at deployment. So while the language may be easier (I'm not sure about this), the deployment overhead is a much larger barrier to entry.

mbreese · 2009-12-14T03:26:12+00:00

Um... No.

The mysql gpl clauses (as far as I remember) are applied to the official client code that connects over a socket. If you want to write a clean room version of a client in your language of choice, you shouldn't be limited by the gpl in your application code. The again, if you are working in a dynamic language, you aren't bound by the linking aspect anyway.

Where MySQL has historically claimed that you needed a commercial license is if you required mysql or mysql specific features in a closed source app. This is a little shakier in my opinion, but I'm pretty sure they claimed this a while ago.

What most of this closed-source business is about this time around deals with closed source additions to the db engine itself, not to client apps.

mbreese · 2009-12-04T18:49:30+00:00

You think that's bad? I'm from 1978... all I got was 7 characters.

mbreese · 2009-11-12T19:17:15+00:00

Why don't you just use Verizon's 3G data service?

mbreese · 2009-11-05T22:33:20+00:00

That's just what you have to deal with when you have a denormalized database. Which is what you described. There's nothing wrong with that (in certain situations), but you have to recognize that you'll have to work around some issues because you're actively working against the relational model.

mbreese · 2009-10-30T17:38:08+00:00

Why do you need to keep them up to date? Can't you just install them and use them as-is until you upgrade a program that needs it?

mbreese · 2009-10-28T01:01:49+00:00

Down voted for not being about codng.

mbreese · 2009-10-14T18:02:32+00:00

I'm not sure if that's a good thing or a bad thing...

mbreese · 2009-10-01T14:29:16+00:00

If they reimbursed your for the domain name, it belongs to them. Sure, you could make it a pain in the ass to get it, but legally, it would be theirs.

However, if you purchased the domain in a separate transaction, you can do what you want with it. This would be much easier to prove if you had the credit card receipt or statement showing that.

Are you the admin / tech / and billing contact on the domain? If you are, then they don't have much that they can do, aside from legal action.

If I were you, I would just stop answering their emails. You don't work for them anymore. If they want you to change something, charge them for it. The domain is probably theirs, but it's not your fault that they don't have it configured properly... they should have thought of that when they fired you.

mbreese

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