5 ms·

Introducing the Mozilla Science Lab

93 points by Lightning 13y ago

galapago 13y ago
I can't find the concrete idea behind this project..
- Zikes 13y ago
  Many areas of science can be and currently are improved through computing. Folding@Home is a great example of this, as are various projects that aim to use the web to detect planets by having people analyze data for transit anomalies. Unfortunately, many areas of science aren't funded well enough to support a team of CS majors to work with the scientists, and indeed many scientists might not even be able to identify what aspects of their work could be improved through computing. This project seems to be aimed at educating scientists to overcome those hurdles.
  - toufka 13y ago
    Educating us is not the problem. We know. Just not much we can do about it. We don't have funding to hire coders/developers/designers. And even if we did, we'd likely spend it on that new microscope instead. Much of what we need doesn't require computational power, but requires a good input parser, a reasonable UI, and some basic (though absolutely solid) math. And a way to change a whole host of variables used in the computations without too much effort. I have a set of a few projects that a mildly competent coder could bang out in a relatively short period of time that would undoubtedly progress the whole field in which it was aimed. But that's pretty much like 20 people. 20 grad students - their bosses don't care if they count the data by hand over a week, or have a computer do it in 2 minutes. It's not worth anyone's (unpayable) time. So I code it myself - it's crappy, it's rough, but it gets the job done. But no one will ever be able to reuse that code. You hackers want to do something good for the world? Set up a hackathon thing for your local biology/chemistry grad students. In a weekends' time you can write a few open-source apps which would rapidly and noticeably affect the pace of cancer and other basic research.
    - Zikes 13y ago
      That hackathon idea sounds great, and even makes me wonder if it should be rolled into the curriculum of the university, perhaps as an assignment of some sort to an applicable computer education course.
    - jk4930 13y ago
      > biology/chemistry What are the low-hanging fruits I can aim for to get used to the problem domain? What are the relevant pain points that justify some hard thinking and coding? In the end what I have in mind is basically this: http://biomind.com/AI_Against_Aging.pdf http://biomind.com/AI_Against_Aging.pdf
      - Zikes 13y ago
        I've known for a while that Perl is really common in biology, and some Googling led me to a project called BioPerl[1]. It might be worthwhile to port that library's functions into other languages that could be beneficial to scientists, or use them to build specialized compiled tools that don't necessitate writing any code. [1] http://www.bioperl.org/ http://www.bioperl.org/
        jk4930 13y ago
        And there are Biopython, Biohaskell etc., but from what I saw there this is more about bioinformatics (e.g., focus on gene sequencing). I don't know whether those are the problems the parent was talking about. From my experience (interviews) with labs it's more about the workflow (often pretty pre-computer) and quick&dirty software with terrible UI.
        toufka 13y ago
        There are a lot of much more basic (far less sexy) things a basic programmer can do that don't need much power. Being able to access those Biopython/biohaskell libraries entirely from a GUI would aid so many people. If you already know how to use python/haskell/fortran, then there is far less urgency in having a good UI or even using those really basic libraries. But there are a lot of fantastic biologists/geneticists/etc. who can reprogram the genes in a living tissue with alacrity, but run in fear from a command line.
ajays 13y ago
Mozilla seems to have lost focus. Firefox still has massive memory leaks; it's not uncommon for me to come home at the end of the day to find FF using 3.8GB out of the 4GB I have, and my Linux box thrashing like crazy. Typically the culprit is Facebook's homepage. But I'd love to see Mozilla spend their effort on first making Firefox great. Memory leaks in FF aren't a new thing.
- ubernostrum 13y ago
  Perhaps you would be interested in MemShrink and areweslimyet? https://wiki.mozilla.org/Performance/MemShrink https://wiki.mozilla.org/Performance/MemShrink https://areweslimyet.com/ https://areweslimyet.com/
- Zikes 13y ago
  Since this is a project of the Mozilla Foundation, not the Mozilla Corporation, it does not necessarily "steal resources" from the Firefox development team. The Mozilla Corporation is no more or less free to improve the browser based on what the Mozilla Foundation chooses to do in its non-profit capacity, except where the Mozilla Foundation's projects improve on the concepts and ideas of the internet and computing as a whole, such as what this project does.
- sp332 13y ago
  Firefox is really aggressive about memory leaks. In fact in recent versions they kill off certain extensions that leave too much unused data in RAM. You should ask in the #firefox channel on irc.mozilla.org, they would help you track down the problem.
- saraid216 13y ago
  http://journal.neilgaiman.com/2009/05/entitlement-issues.html http://journal.neilgaiman.com/2009/05/entitlement-issues.htm... s/George R. R. Martin/Mozilla/g
glesica 13y ago
Soooo... what exactly do they plan to DO? The entire article is filler, there's no actual information. All I can gather is that they might tell scientists about the "open web", whatever that is. Couldn't they just have done that in the blog post and called it a day?
- toufka 13y ago
  It would be really nice to have an open, human-readable scientific data format. Basically a CSV+ that had a single piece of metadata - uniform mandatory SI units. To be able to read/write/import/export that to and from desktop machines to the web would aid science so much. AND it seems like a perfect job for the Mozilla foundation. I have no idea from their (uninformative) article what they're actually doing...
  - jpallen 13y ago
    I don't really know why human readable is important here, but there already exist open data formats that have good support for the things that matter: large data sets, compression and support for multiple platforms and languages. I'm not very knowledgeable about any, but some I am aware of: http://www.unidata.ucar.edu/software/netcdf/ http://www.unidata.ucar.edu/software/netcdf/ http://cdf.gsfc.nasa.gov/ http://cdf.gsfc.nasa.gov/
    - toufka 13y ago
      Entirely different concept. I want simple data to be easily distributable and interpretable. Make a format that can universally read/write the data in these very basic graphs: http://download.cell.com/images/journalimages/2211-1247/PIIS2211124713001964.gr3.lrg.jpg http://download.cell.com/images/journalimages/2211-1247/PIIS... http://download.cell.com/images/journalimages/2211-1247/PIIS2211124713001721.gr2.lrg.jpg http://download.cell.com/images/journalimages/2211-1247/PIIS... http://download.cell.com/images/journalimages/2211-1247/PIIS2211124712004299.gr4.lrg.jpg http://download.cell.com/images/journalimages/2211-1247/PIIS... Most science (that really needs hackers' help) is not the big sexy datasets, but the really basic HTML5/CSS viewable graphs otherwise done in Excel. But it must be done in a scientifically rigorous way (retain units and labels, be able to manipulate those units, and be able to show/hide data between different datasets). Think a way to download and view a melting point curve dataset without ANY user configuration. Or an enzyme activity curve. Or a drug dosage response curve. VERY basic data, but it must be able to maintain and interpret a label and a unit in addition to the number itself.

93 points by Lightning 13y ago

galapago 13y ago

I can't find the concrete idea behind this project..

Zikes 13y ago
Many areas of science can be and currently are improved through computing. Folding@Home is a great example of this, as are various projects that aim to use the web to detect planets by having people analyze data for transit anomalies. Unfortunately, many areas of science aren't funded well enough to support a team of CS majors to work with the scientists, and indeed many scientists might not even be able to identify what aspects of their work could be improved through computing. This project seems to be aimed at educating scientists to overcome those hurdles.
- toufka 13y ago
  Educating us is not the problem. We know. Just not much we can do about it. We don't have funding to hire coders/developers/designers. And even if we did, we'd likely spend it on that new microscope instead. Much of what we need doesn't require computational power, but requires a good input parser, a reasonable UI, and some basic (though absolutely solid) math. And a way to change a whole host of variables used in the computations without too much effort. I have a set of a few projects that a mildly competent coder could bang out in a relatively short period of time that would undoubtedly progress the whole field in which it was aimed. But that's pretty much like 20 people. 20 grad students - their bosses don't care if they count the data by hand over a week, or have a computer do it in 2 minutes. It's not worth anyone's (unpayable) time. So I code it myself - it's crappy, it's rough, but it gets the job done. But no one will ever be able to reuse that code. You hackers want to do something good for the world? Set up a hackathon thing for your local biology/chemistry grad students. In a weekends' time you can write a few open-source apps which would rapidly and noticeably affect the pace of cancer and other basic research.
  - Zikes 13y ago
    That hackathon idea sounds great, and even makes me wonder if it should be rolled into the curriculum of the university, perhaps as an assignment of some sort to an applicable computer education course.
  - jk4930 13y ago
    > biology/chemistry What are the low-hanging fruits I can aim for to get used to the problem domain? What are the relevant pain points that justify some hard thinking and coding? In the end what I have in mind is basically this: http://biomind.com/AI_Against_Aging.pdf http://biomind.com/AI_Against_Aging.pdf
    - Zikes 13y ago
      I've known for a while that Perl is really common in biology, and some Googling led me to a project called BioPerl[1]. It might be worthwhile to port that library's functions into other languages that could be beneficial to scientists, or use them to build specialized compiled tools that don't necessitate writing any code. [1] http://www.bioperl.org/ http://www.bioperl.org/
      - jk4930 13y ago
        And there are Biopython, Biohaskell etc., but from what I saw there this is more about bioinformatics (e.g., focus on gene sequencing). I don't know whether those are the problems the parent was talking about. From my experience (interviews) with labs it's more about the workflow (often pretty pre-computer) and quick&dirty software with terrible UI.
        toufka 13y ago
        There are a lot of much more basic (far less sexy) things a basic programmer can do that don't need much power. Being able to access those Biopython/biohaskell libraries entirely from a GUI would aid so many people. If you already know how to use python/haskell/fortran, then there is far less urgency in having a good UI or even using those really basic libraries. But there are a lot of fantastic biologists/geneticists/etc. who can reprogram the genes in a living tissue with alacrity, but run in fear from a command line.

ajays 13y ago

Mozilla seems to have lost focus. Firefox still has massive memory leaks; it's not uncommon for me to come home at the end of the day to find FF using 3.8GB out of the 4GB I have, and my Linux box thrashing like crazy. Typically the culprit is Facebook's homepage. But I'd love to see Mozilla spend their effort on first making Firefox great. Memory leaks in FF aren't a new thing.

ubernostrum 13y ago
Perhaps you would be interested in MemShrink and areweslimyet? https://wiki.mozilla.org/Performance/MemShrink https://wiki.mozilla.org/Performance/MemShrink https://areweslimyet.com/ https://areweslimyet.com/
Zikes 13y ago
Since this is a project of the Mozilla Foundation, not the Mozilla Corporation, it does not necessarily "steal resources" from the Firefox development team. The Mozilla Corporation is no more or less free to improve the browser based on what the Mozilla Foundation chooses to do in its non-profit capacity, except where the Mozilla Foundation's projects improve on the concepts and ideas of the internet and computing as a whole, such as what this project does.
sp332 13y ago
Firefox is really aggressive about memory leaks. In fact in recent versions they kill off certain extensions that leave too much unused data in RAM. You should ask in the #firefox channel on irc.mozilla.org, they would help you track down the problem.
saraid216 13y ago
http://journal.neilgaiman.com/2009/05/entitlement-issues.html http://journal.neilgaiman.com/2009/05/entitlement-issues.htm... s/George R. R. Martin/Mozilla/g

glesica 13y ago

Soooo... what exactly do they plan to DO? The entire article is filler, there's no actual information. All I can gather is that they might tell scientists about the "open web", whatever that is. Couldn't they just have done that in the blog post and called it a day?

toufka 13y ago
It would be really nice to have an open, human-readable scientific data format. Basically a CSV+ that had a single piece of metadata - uniform mandatory SI units. To be able to read/write/import/export that to and from desktop machines to the web would aid science so much. AND it seems like a perfect job for the Mozilla foundation. I have no idea from their (uninformative) article what they're actually doing...
- jpallen 13y ago
  I don't really know why human readable is important here, but there already exist open data formats that have good support for the things that matter: large data sets, compression and support for multiple platforms and languages. I'm not very knowledgeable about any, but some I am aware of: http://www.unidata.ucar.edu/software/netcdf/ http://www.unidata.ucar.edu/software/netcdf/ http://cdf.gsfc.nasa.gov/ http://cdf.gsfc.nasa.gov/
  - toufka 13y ago
    Entirely different concept. I want simple data to be easily distributable and interpretable. Make a format that can universally read/write the data in these very basic graphs: http://download.cell.com/images/journalimages/2211-1247/PIIS2211124713001964.gr3.lrg.jpg http://download.cell.com/images/journalimages/2211-1247/PIIS... http://download.cell.com/images/journalimages/2211-1247/PIIS2211124713001721.gr2.lrg.jpg http://download.cell.com/images/journalimages/2211-1247/PIIS... http://download.cell.com/images/journalimages/2211-1247/PIIS2211124712004299.gr4.lrg.jpg http://download.cell.com/images/journalimages/2211-1247/PIIS... Most science (that really needs hackers' help) is not the big sexy datasets, but the really basic HTML5/CSS viewable graphs otherwise done in Excel. But it must be done in a scientifically rigorous way (retain units and labels, be able to manipulate those units, and be able to show/hide data between different datasets). Think a way to download and view a melting point curve dataset without ANY user configuration. Or an enzyme activity curve. Or a drug dosage response curve. VERY basic data, but it must be able to maintain and interpret a label and a unit in addition to the number itself.