
Banyan, the "GitHub of Science", is now in public beta - twog
http://blog.banyan.co/banyan-is-now-in-public-beta/
======
simonster
How does your product compare with <http://www.openscienceframework.org/>? As
a scientist, I'm inclined to trust OSF more, since it's run by other
scientists, fully open source, and doesn't need to make a profit. At the
moment, OSF seems more focused on tools to facilitate collaboration and less
focused on replicating functionality currently available on GitHub, although
it sounds like they use git as a backend and eventually plan to implement
functionality similar to what Banyan (and GitHub) currently provide.

~~~
dkural
I'm a recovering PhD. OSF looks pretty cool.

By the way OSF costs money if it is done by scientists. Those scientists get
paid by someone. They spent shit ton of money (in form of salaries + time)
building it + publishing it. Science works on government grants, i.e. taxpayer
money. It is actually a fairly profitable industry, and NIH grants are the
biggest contributor to capital expenditure of US Research Universities. The
55% overhead coming out of each grant is basically the "profit margin".
Calling something by a different name doesn't make it so. Your github profile
says you're at MIT, around Cambridge. So am I. What do you think pays for all
the shiny buildings around Kendall? It's not just philanthropy.

~~~
simonster
Sure, OSF costs money, but VC-funded startups are under pressure to monetize
their customer bases, whereas grant-funded projects just need to make
something useful enough to justify continued investment. There's the obvious
risk is that a VC-funded company will make its money off of selling your
private information. (I don't think this is very likely, but I trust Brian
Nosek a lot more than I trust most startups.) The bigger issue is that VC-
funded companies need to keep a tight leash on their product, whereas grant-
funded projects are free to grow in a distributed fashion. While ordinary
people are happy to live within the limits of their software, scientists like
to explore new frontiers, and it sucks when our software can't take us there.
This is why I firmly believe that software (and preferably hardware) that
scientists use to do science needs to be open source.

I'm not sure I'd call grant income that gets reinvested in infrastructure and
educational expenditures "profit." Not only do private corporations buy shiny
buildings, but they also have a legal obligation to make as much money for
their shareholders as they possibly can. MIT doesn't.

~~~
wamatt
While I can agree with the spirit of your message, OTOH...

 _> Not only do private corporations buy shiny buildings, but they also have a
legal obligation to make as much money for their shareholders as they possibly
can._

This seems to be a popular belief, but it's simply not true. Private companies
have no legal requirement to make profits or pay dividends. Even public
companies, do not have to by law, maximize profits ("make as much money").[1]
Corporate officers do of course, have an obligation to act in the best
interests of the company, and have maintain certain fiduciary duties.

 _[1][http://skeptics.stackexchange.com/questions/8146/are-u-s-
com...](http://skeptics.stackexchange.com/questions/8146/are-u-s-companies-
legally-obligated-to-maximize-profits-for-shareholders*)

~~~
simonster
Sorry, you're right, there is no direct legal obligation to make money.
However, investors in startups frequently have a large degree of control over
the direction of the company, and often care more about the bottom line than
any broader mission to change the world. See e.g. Jason Hoyt's blog post on
Mendeley: [http://enjoythedisruption.com/post/47527556151/my-
thoughts-o...](http://enjoythedisruption.com/post/47527556151/my-thoughts-on-
mendeley-elsevier-why-i-left-to-start)

------
songgao
This is a great idea!

I've been trying to collaborate my professor on academic papers with git. We
tried my own git server, github, but they still seem to be too much trouble
for people who do not use git regularly. Online LaTex editor integrated with
the git service would be great! It would be better if you could add code
highlight in the editor though. Also realtime PDF preview (maybe not
realtime.. it'll be overwhelming for the server. A compile button?) would be
awesome!

And for sure we need a separate community from Github just for academic
publications. Mixing softwares and papers altogether is not a good idea.
Banyan is really cool!

Congratulations on launching!

~~~
twog
Thanks songgao! Drop an email (mine is in my profile) and Ill get you signed
up on our git-powered latex editor. It has most the features you just
described, and is launching soon =)

~~~
zmjones
I would really like access to this too. I have been using sharelatex and the
git support is still not there. My email is zmj@zmjones.com

~~~
twog
Thanks! Will do. I will drop you a line this afternoon

------
cing
Great to see another product in this space (<https://www.scigit.com/> launched
not too long ago). As far as writing papers, my old-fashioned P.I. will
probably never budge from Microsoft Word, so Google Docs is the best solution
at the moment. The fact that they have "Google Scholar" integration for
inserting citations into the editor makes it pretty much a no brainer for
writing a draft.

~~~
beambot
Yikes! What field are you in? For most STEM folks, TeX seems to be pretty
standard. I'd really love to see a collaborative TeX editor (web based?).
Better yet... a collaborative emacs!

~~~
cing
I'm in biology. The journals Nature and Science both specify that Microsoft
Word is their preferred format for submissions and I'd be surprised if lots of
others still do. Collaborative online TeX editors have been featured on HN
before (<https://www.writelatex.com/>, <https://www.sharelatex.com/>).

------
twog
Hi HN!

We launched a private version of Banyan to a few of you here months ago. Since
then, our team has been hard at work trying to make Banyan the future of open
science. Todays launch is just the start.

We know we have alot of work to do. Over the next few months we plan to tackle
science, reproducibility, and make existing tools more awesome through our
API.

I want to be as transparent as possible. Im happy to answer any questions you
might have.

~~~
killahpriest
Congrats! Unfortunately, your server isn't handling the load and the google
cache is a SASS error.
[http://webcache.googleusercontent.com/search?q=cache:knsEMz3...](http://webcache.googleusercontent.com/search?q=cache:knsEMz3EwecJ:https://banyan.co/+&cd=4&hl=en&ct=clnk&gl=us)

Got something more descriptive you can link to?

~~~
twog
Sorry, we cross posted to reddit & HN and the response has been outstanding.
Working on getting this fixed right now.

~~~
twog
Blog is back up! Sorry about that everyone

------
RK
Are you planning on releasing a Linux client?

When you say science, git, and LaTeX, Linux is often the next word in the
sequence...

------
zmmmmm
its kind of tragic that I read that whole post, spent another 5 minutes
researching, trying to find some kind of more information, but _I still have
no idea what this tool actually does_.

~~~
_fs
Didnt you get the memo? Its like twitter for facebookers using science with
github

------
jmmcd
I don't get it. I can't see any information on the homepage that makes it
different from just using github.

~~~
twog
Our main two differences from github is that we built banyan to be version
control for "humans". Our mac application for example is extremely simple to
use, and was designed with an 18 year old undergraduate/55 year old lab
veteran in mind. Banyan was designed to be the middle ground of collaboration
for users who know git with people who have no idea what git is (and in most
cases, cant be bothered to learn another tool).

Our second difference is our focus on scientific specific tools like latex,
ipython, etc.

~~~
stared
So, are you going to provide built-in things like: IPython viewer (like
<http://nbviewer.ipython.org/>), LaTeX viewer for notes (like
<http://mathb.in/>), support for slides (this thing would be awesome - to have
possibility to view them and view/fork their source; a bit related to
<http://slidewiki.org/>) or something in that line?

~~~
twog
We have similar ideas for integrations with those tools, with the exception of
latex. With latex, we have our own online editor with some neat git
integration.

~~~
leehro
Do you have any examples of these online? Today, I don't see any reason I
would use this over GitHub.

I gather that your Mac app may be simpler, but it's not available yet.

Since I don't already have dozens of projects on banyan, it's hard to see the
value.

Perhaps it would be a good idea to link to some repos with examples of the
fancy LaTeX or IPython formatting

------
xroja
Have you thought about easing distributed collaboration for structured data?
The use case I'm thinking of is multiple groups submitting data to one central
informatics/analysis group (i.e. consortia, meta-analyses). Scientists still
throw around data in excel sheets with ever-increasing versioning through file
names (e.g., gene.data.v29.201230429.janes.final.Final.reallyFinal.xls). It's
a huge time-suck that doesn't help anybody. Support for easy viewing of XML,
JSON, or even some sort of hosted RDBMS would be incredible.

I think it's great to target the wider, non-developer audience. They could
benefit immensely from version control, distributed systems, and smart editing
tools. It could be a big benefit to the whole scientific community.

~~~
twog
Im really interested in this but have some questions I would like to ask you.
Do you mind dropping me an email at toni (at) banyan.co?

------
irollboozers
Congrats, this looks great! Some of the buttons are a little off
(<http://i.imgur.com/9CRvFQj.png>) Mac OS X, Chrome 26.0.1410.65.

I'm very excited to tell people that github for science is now a thing. I'll
be signing up for sure.

~~~
twog
Thanks! Just submitted a fix for this. We will push this into production when
things slow down on HN a little bit

~~~
irollboozers
No problem, the firehose that is HN is definitely exciting. Hope you guys are
getting good traffic :)

------
Osmium
Would love to try this but you'd have to let me have at least 1 private
project. I don't have permission to share private research data with the
world.

Also, I tried to submit my email to be notified for the mac app and was told
it was invalid (it was just a standard @gmail address).

~~~
twog
Hi Osmium, thats a good point. We will revisit the pricing model tonight.

The forms are broken unfortunately. I have submitted a fix, but we wont be
deploying until later tonight when the HN craziness slows down. In the
interim, you can drop me your email at toni (at) banyan.co and I will manually
add it to the list

------
pmtarantino
I don't know if you were inspired by a submission [1] I did almost six months
ago, but if not, kudos anyway :) When the site is up again I will check it!

[1]: <https://news.ycombinator.com/item?id=4712787>

~~~
twog
It wasnt! But we should talk. We are looking for engineers who want to change
the way science works. We announced Banyan publicly last August [1] during the
<http://thegigtank.com>

[1] <http://us-ignite.org/2012/08/gig-tank-demo-day-delivers/>

~~~
pmtarantino
Oh, I see, and I am checking the website right now. It something different
from what I thought, but it is cool anyway. My email is on my profile :)
Congratulations again!

------
stared
Is there a way to make repository which is partly private? For me it is a
common use-case where some data aren't share for any reason (e.g. because they
are not checked yet whether they are correct), while other files are public?

~~~
twog
Not currently, but this is a great idea. We may just have to add this to the
roadmap

~~~
songgao
The other thing is that, IMHO, private repo for this is not good for academic,
instead, make it temporarily private. People write papers to get published.
They surely want as many people as possible to see it. The reason they want it
to be private is to hide it from others before getting published so the ideas
won't get stolen. So I'm thinking maybe set up a time limit for repos being
private would be better? After that time limit, the repo is automatically made
public unless requested more time by user.

~~~
stared
It is one reason. But e.g. in my field (theoretical physics) I am not afraid
of theft (well, if someone is smart enough to understand and polish a half-
written paper, then (s)he can write much better stuff) but of things that "as
of now makes sense only to me" or "there are half-written" (e.g. in some
places I changed indices i to i+1, but not in all, making it both frustrating
and useless to read) or may simply be false and I don't want to publish it
before checking (e.g. plots may be completely wrong because of a typo).

Anyway, a time limit is a good idea.

And anyway, when there are timestamps, it's harder to steal an idea. It
actually may encourage people to write notes on things to do, share some
partial proofs, etc

~~~
saraid216
Why a time limit? Why not a "publish" button that flips it to public? (And
maybe submits it to arXiv at the same time, optionally.)

~~~
stared
Integration with arXiv (i.e. "sent to arXiv" or "get source from arXiv") would
be great. And yes, just a button "publish" would be convenient.

------
up_and_up
Clicking on either screenshot in the blog post takes me to a new page with a
smaller version of the screenshot ([http://blog.banyan.co/banyan-is-now-in-
public-beta/dashboard...](http://blog.banyan.co/banyan-is-now-in-public-
beta/dashboard-banyan/)). Then I have to click the image again to see:
[http://blog.banyan.co/wp-
content/uploads/2013/04/Dashboard-B...](http://blog.banyan.co/wp-
content/uploads/2013/04/Dashboard-Banyan.png)

Wouldnt a better interaction be to display a larger screenshot on the first
click? Thats what I would expect?

~~~
twog
Yes it should! Sorry about that. Just fixed it for you if check it now!

~~~
up_and_up
Cool. Thanks.

------
dfinninger
This isn't a publishing platform, right? I'm all about free data, but if some
"scientists" decide to "publish" their paper on your site it seems like that
would totally evade peer-review. I know that is not your intention, but do you
worry that some people my try to put out results that have not been fully
tested/peer-reviewed? There are non-peer-reviewed journals (my mom finds them
all the time...) out there, but a free easy platform seems like some people
might try to take advantage of this system.

~~~
VLM
"some people"

Oh, just call a marketing guy a marketing guy.

I'll have to look into how it manages trust, for things like this.

------
dheavy
Great initiative! But I find the screencaps on the landing page's slideshow
very misleading imho. It displays some code repo... ok, now I'm a coder and
just like others I'd be then inclined to ask myself "why would I use this
instead of Github or Bitbucket?". And my gf is a neuroscientist and her gut
reaction was "well... I don't code, how is this of any interest for me? I
don't get it...".

~~~
dheavy
Just to be clear: we both are VERY interested by this site, and actually quite
excited. It's better than any other related initiatives and we expect to try
it out asap! It's just this detail made us tick...

~~~
twog
I agree we need to clean that up. We use a rake command to seed our test
server with test data. We will swap those out for some real screenshots today

~~~
dheavy
We're registering. I've passed the word to other fellow scientist in my
network. Looking forward to use it fully.

------
zmjones
I am hopeful that this works, as my collaborators can definitely not be
bothered to learn git. The UI elements are way too big IMO.

~~~
twog
Hi zm. What do you mean by the UI elements? Do you mind snapping a screenshot
for me?

~~~
zmjones
The nav bar and the commits page are too big I think. There ends up being a
lot of space wasted. The commits page especially so. 5 commits should easily
fit on a page. There are also two date information fields. One listing how
many days ago the commit occurred and the other indicating what date the
commit occurred on.

~~~
twog
Thank you for the design feedback. I take ux/ui feedback very seriously. I
have passed this onto our designer

------
willbarkis
To Toni & the whole Banyan team, CONGRATS on launching the public beta! I'm
excited to see Banyan on the gigabit web. :)

~~~
twog
Thanks Will!

------
Maro
It's built on top of git?

~~~
twog
Hi Maro, yes it is.

------
bborud
Within the first 60 seconds your site does not answer the question "why would
I want to use this rather than Github?". I'm not sure most people will spend
even 60 seconds trying to find an answer to that question, so you might want
to figure out a way to show/tell.

------
moyix
Is there any way to create an anonymized link to a set of data and
experimental results? Right now I'd love to use this, but all the conferences
I submit to are double-blind, so there's no good way to let reviewers have
access to my experimental data...

~~~
VLM
And, this is the other side of the trust coin. Who's data and is it the "real"
data. (obviously I don't mean you personally but more like scientists
generally)

------
TrevorBurnham
Congratulations on launching! I applied to YC a few years ago with a similar
concept. Your site looks gorgeous, and I'm excited to see it develop. I hope
you succeed in disrupting a space that's been neglected for far too long.

------
twog
Sorry the blog is down everyone! <http://Banyan.co> can provide a little more
info while we scramble to get this back up!

------
skkdkk
How do i delete my account? I created one to check it out, but didnt realise i
would not be able to hide my name or email address...

------
csmatt
This is great. Too often we only get the original researchers' interpretation
of the data and not much else. Good luck with it!

~~~
twog
Thanks csmatt, I completely agree!

------
dopamean
I first heard of you guys when I read an interesting post about the startup
scene in Chattanooga. Congrats on launching.

~~~
haney
If you haven't checked in lately the scene is Chatt is growing daily
<http://noogastartups.com/>

------
GhotiFish
Off topic: Dear banyan blog. I can't read your text!

No greater than #888 on a white background, otherwise you have to bold the
text.

------
batty
I tried to leave my email regarding the Windows port and it said my email
address was invalid.

------
raffenet
it looks like this just runs a local gitlab instance on your mac. how do you
share with other users?

~~~
sciencerobot
There is a central GitLab server.

~~~
raffenet
So the blog post claims improvements to the webapp were made and has an image
of the gitlab interface. Gitlab was recently updated and made big changes in
the backend to improve performance.

This smells fishy.

~~~
twog
Hi raffenet,

We have used gitlab components & also contributed back to gitlab. Its a great
project, but I can assure you we have an entirely different product. Were just
leveraging OSS projects like any other startup

~~~
mugsie
from what I can see it is a Gitlab 5 install with a skin? What advantage is
there for an organisation using your product vs a free gitlab install?

------
bdunbar
Banayan .. github ..

Hurray - VINES is finally open sourced!

"GitHub of Science"

Aw.

~~~
cbsmith
I was wondering who else immediately leaped to Banyan Vines!

~~~
bdunbar
How could I not?

My first job in IT, I got tossed into the deep end of LAN administration -
sink or swim - and Banyan was the pool.

