Forum: Bioinformatics Mobile App
2
gravatar for aeinsights
4.7 years ago by
aeinsights20
aeinsights20 wrote:

Hi Everyone,

 We are in the process of creating bioinformatics mobile applications. Rather than common app we want to give app for scholars and scientist for them to access the data wherever they and whenever they want.

Please give your suggestions and recommendations to pick the area or functionalties need to be implemetned.

 

Thanks.

ADD COMMENTlink modified 3.4 years ago by Dan D6.8k • written 4.7 years ago by aeinsights20
3

This and the related thread is getting a bit out of hand in that they are getting too personal. I would suggest that we all take a break from it for a few days.

I wish the authors success with their app.

Regardless of what value someone might associate with their product at this stage it really seems that the authors have good intentions and are just inexperienced in this field. Perhaps, rather than posting a followup the authors might just want to go back to the drawing board and reflect on why people's perceptions of this product ended up so different than that of the creators. And in the future try to avoid the path that lead that way. There are many lessons there.

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by Istvan Albert ♦♦ 80k
7
gravatar for Emily_Ensembl
4.7 years ago by
Emily_Ensembl18k
EMBL-EBI
Emily_Ensembl18k wrote:

In Ensembl we're currently looking into a mobile website (not an app) and are asking ourselves similar questions. We don't envisage anybody doing proper analysis on a phone as 5heikki has already stated, but we imagine something more like a quick gene look-up when chatting over coffee or in a conference. If anybody does or has tried to look up this kind of data on a phone, we'd be interested to know about the kinds of things you were looking up.

ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by Emily_Ensembl18k

Hi Emily,

 Great to hear... Can we talk, I need some information on this.. Thanks.

ADD REPLYlink written 4.7 years ago by aeinsights20
1

What do you want to know?

ADD REPLYlink written 4.7 years ago by Emily_Ensembl18k

My lab would benefit from a quick look for a gene, its variants with effects predicted for each variant - something like HGMD, but for mobile devices. Any serious discussion after that is gonna happen on my Mac.

ADD REPLYlink written 4.7 years ago by RamRS22k

Hi Emily, this is indeed how I use most often my smart-phone and tablet for biology: getting more info about a molecule/structure/disease etc. during seminars or even group meeting.
 

ADD REPLYlink written 4.7 years ago by Arnaud Ceol840
5
gravatar for Istvan Albert
4.7 years ago by
Istvan Albert ♦♦ 80k
University Park, USA
Istvan Albert ♦♦ 80k wrote:

I think this is a counter example to implementing a software.

It is very unlikely that you could implement a  useful tool if you don't know what people need to begin with. You should have to have a basic utility and mode of operation in mind and the feedback that you seek should be on adapting and tuning that.

ADD COMMENTlink written 4.7 years ago by Istvan Albert ♦♦ 80k
6

I think they're trying to use us for free market research. "Give us an interesting idea for something we can then sell to you..."

ADD REPLYlink written 4.7 years ago by Devon Ryan91k

Its not about free market research its about getting know the users.

ADD REPLYlink written 4.7 years ago by aeinsights20

We have N number of plans from basic view to mutation pipelines. But what wanted to understand who needs what. It is always good to understand what people need.

ADD REPLYlink written 4.7 years ago by aeinsights20

There are quite a few online pipelines, but what is the benefit of mobile apps here? I'm pretty sure any bioinformatics person that can operate a mobile app already is using VPN to connect to their high power work machines and/or clusters/HPCs.

ADD REPLYlink written 4.7 years ago by RamRS22k

Ram, I can understand the pain point you are having from your previous experiences. As most of them said here, UIX matters. Can you please let me know what are the pipelines are available at present?

ADD REPLYlink modified 13 months ago by RamRS22k • written 4.7 years ago by aeinsights20
4
gravatar for Dan D
3.4 years ago by
Dan D6.8k
Tennessee
Dan D6.8k wrote:

Here's my problem: you've shown and now admitted that your knowledge of bioinformatics is lacking. At the same time you're peppering us with absurd promises and asking us to invest our time in a product for whose existence we don't yet have real evidence. Your very attractive template-based website that slickly obscures any specifics of the underlying product only furthers this perception. I especially like the pineapple non-sequitur at the end.

I'm thinking you're trying to get seed money from some person or organization by roping a few of us into signing up for your platform and using those signups as evidence of involvement and interest from the greater bioinformatics community. Maybe I'm wrong, but so far this whole thing seems to be a waste of our time and possibly fraudulent. Thus I feel compelled to call you on it.

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Dan D6.8k

Thanks @Dan, For your wonderful assumption. This is how you react when someone asking for suggestions and recommendations.

  1. I never ask anyone to spend their time, if they don't want and not interested.
  2. I don't want get something out of silky thing without the context as I said we are in beta.
  3. I don't even thinking of seed money, which is not even in my thought. Thanks for reminding me.
  4. Without knowing something don't make comment on credibility

If you still open to assists us, please otherwise thanks lot.

ADD REPLYlink written 3.4 years ago by support50
3
gravatar for Pierre Lindenbaum
4.7 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum121k wrote:

"What's the current state of my bwa alignment"

ADD COMMENTlink written 4.7 years ago by Pierre Lindenbaum121k

This is the ONLY implementable suggestion here :)

ADD REPLYlink written 3.4 years ago by RamRS22k
3
gravatar for 5heikki
4.7 years ago by
5heikki8.4k
Finland
5heikki8.4k wrote:

Underwhelming performance, a tiny display, plain awful input.. yeah bioinformatics apps on mobile devices sounds like a great idea. A very creative person could maybe come up with useful companion apps to real programs.. other than that. No.

ADD COMMENTlink written 4.7 years ago by 5heikki8.4k
2
gravatar for RamRS
4.7 years ago by
RamRS22k
Houston, TX
RamRS22k wrote:

The only time I've used a mobile device (I used a tablet, not a phone) to do anything related to actual bioinformatics work was when I SSH'd into my HPC and ran a qstat. Most of my work is done in the terminal and almost all of it involves Control keys (Cmd/Ctrl/Alt/Opt/Esc/Tab) - IMO a mobile interface will only serve to slow me down and irritate me.

Mobile interfaces are amazing when an application is UX intensive, but for data intensive/pipeline oriented tasks, I highly doubt any app would help.

TL;DR: Plain text manipulation is a nightmare on mobile devices. So, mobile apps are not really helpful.

ADD COMMENTlink written 4.7 years ago by RamRS22k
2
gravatar for Daniel
4.7 years ago by
Daniel3.7k
Cardiff University
Daniel3.7k wrote:

The only useful application I could imagine for mobile devices would be data visualisation i.e no actual informatics processing. 

If I could get a genome browser app on my 10 inch tablet, or have it be chromecast enabled so I can push it to the TV then that'd be interesting.

ADD COMMENTlink written 4.7 years ago by Daniel3.7k

This is awesome Daniel... This is one way of using it... We will take note of this.

ADD REPLYlink written 4.7 years ago by aeinsights20

You can kind-of get this with Biodalliance (http://www.biodalliance.org/human37.html) which is web-based and on the iPad that's full screen :)

ADD REPLYlink written 3.4 years ago by John12k
2
gravatar for Dan D
3.4 years ago by
Dan D6.8k
Tennessee
Dan D6.8k wrote:

I'd be interested in API-directed ultra-short-read de novo assembly of low-coverage FFPE data. Is this something your group has experience with?

ADD COMMENTlink written 3.4 years ago by Dan D6.8k
1

Nice one, Dan. You should have asked for a pony, too!

ADD REPLYlink written 3.4 years ago by harold.smith.tarheel4.4k

I'm here to look for the feedbacks and need of industry. Be open minded, can you tell me single tool, which has rich in terms of UI and features for Bioinformatics and affordable by everyone.

For us its all data and process with subject matters experts. if you don't know let me tell you, we build a pipeline for a customer. Which was seen as a challenge some of big players. If you don't know or not open to share your thoughts it's good to stay away.

Are you open for the challenges? We are and we will deliver if we are committing something.

Thanks.

ADD REPLYlink written 3.4 years ago by aeinsights20
2

I feel like this is actually poetry but the world just isn't ready for it yet.

ADD REPLYlink written 3.4 years ago by John12k
1

You realize there's a reason why most bioinformatics tools don't have a flashy UI, right? I cannot help it if you equate flashy GUI to "good UX". They are not the same. UI should work the way users want it to.

In our case, automation and programmability takes precedence over graphical toggles. We're not interested in typing bwa commands or picking BLAST options off a UI 400 times a week or reading through pages and pages of GATK's best practices.

We do it once, write a bunch of make files that do this stuff for us and then write a bunch of configuration files that inform the make files. To be able to do that, we have to stick to institution specific idiosyncrasies - such as the HPC system, the batch schedulers, the environments, user auth etc.

While a website for the topmost layer would be useful to a high throughput lab that handles an entire organization's internal and external requests, I do not see individual users benefitting from a low-customization environment. And while I can automate/copy-paste+modify commands, I cannot do that with app interactions as easily.

That aside, now that you have committed to the de novo ultra short read assembly with an API for low coverage data (oh the horror - Dan D , you're truly magnificently evil), I'd love to see how you're going to deliver that.

Guys, NEVER agree to something you do not understand.

ADD REPLYlink written 3.4 years ago by RamRS22k

Yeap Dan, We can enable this feature. The same can be hosted both in private or public mode. Please write to support@bioelm.com with more information on you need. We are happy to enable this feature for you.

Thanks.

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by aeinsights20
2

All I can say is ¯_(ツ)_/¯

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by Dan D6.8k

Dan, I didn't get you.

ADD REPLYlink written 3.4 years ago by aeinsights20
1

¯_(ツ)_/¯ was Dan's polite emoticon for 'WTF?'.

ADD REPLYlink written 3.4 years ago by harold.smith.tarheel4.4k

I'm really stoked that you can do this! I always thought it was impossible. In fact I was sure of it. Now that you've shown just how amazing your software is I'm sure more people here will have their own big challenges.

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by Dan D6.8k

Dan, Why don't you share few more information on this and we can work together? Please share you thoughts. aeinsights is one of the developer from our team. Thanks.

ADD REPLYlink written 3.4 years ago by support50
4

This is really the problem with your approach, you don't actually know bioinformatics.

Dan has stated a nonsensical problem to see if you can tell nonsense from actual science.

When you said yes we'll get right on it and that you can enable the feature right away you kind of tell us that you don't really understand this field.


But I do actually have a serious proposal that would make me drop anything and seriously investigate your services and become a fan.

  1. Pick a published bioinformatics analysis from a high impact paper. Pick a glam journal: Nature, Science that gets people's attention.
  2. Reimplement their pipeline in bioelm. Starting from raw data have it produce and visualize some (at least one) of the main findings of this paper.
  3. Demonstrate how users now can do this analysis from their phone.
  4. Have a push notification that says: "Nature Paper reanalysis completed in 5 minutes." now that would get my attention ... :-)

If you do this I'll be your fan. I am sure many people here would love to give you suggestions which paper to implement.

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by Istvan Albert ♦♦ 80k
2

Oh my stars, this just gets better and better.

ADD REPLYlink written 3.4 years ago by Dan D6.8k

Guys, I just want to understand why this is not feasible. Can someone please answer? I'm not a subject matter expert of Bioinformatics. Why we can't access FFPE data and expose them over API?

Thanks,

ADD REPLYlink written 3.4 years ago by aeinsights20

You can access FFPE data and expose it over an API - that's called file hosting. Try hosting a de novo assembler. Try designing one that works with short reads, let alone ultra short reads. Then try dealing with low coverage.

Exposing files over API is so simple that it takes maybe 10 minutes to do that.

ADD REPLYlink written 3.4 years ago by RamRS22k

Yeap I'm not expert in bioinformatics but I can follow when subject matter explain me what it is all about. That's the reason I'm more eager to get beta customers, who can start using our platform.

Sure will make you as fan of our platform... so soon.. :)

ADD REPLYlink written 3.4 years ago by support50

Dan, Can you share the data if you have, we will host them for free with graphical representation of data and make it available for both web and mobile. Thanks.

ADD REPLYlink written 3.4 years ago by aeinsights20
2

Err, Dan wasn't making a serious proposal; he was having a bit of fun at your expense.

ADD REPLYlink written 3.4 years ago by Devon Ryan91k

@Dan, I am startup and not an enterprise to have fun around here :)

ADD REPLYlink written 3.4 years ago by support50
2

Guys, honestly, if you're looking to build credibility, you're going about it the wrong way. This latest commitment misstep has pushed your claims from "unbelievable" to "highly ridiculous". That's why people are having some good natured fun at that expense.

ADD REPLYlink written 3.4 years ago by RamRS22k

Ram, We are validating and we want to ensure we are addressing real problem.

So can you please answer what are difficulties in exposing FFPE data over API. I will accept your assumptions and conclusions post your answer.

Thanks,

ADD REPLYlink written 3.4 years ago by support50
1

The FFPE data isn't even the main point.. The ultra short and low coverage just doesn't play nicely with denovo assembly. If you can do it, then I guess we have been wasting our time in bioinformatics for the past decades....

ADD REPLYlink written 3.4 years ago by Sam2.4k

Thanks Sam, I really missed denovo assembly. That's the catchy here...

Let me spend sometime on this and get back to you.

ADD REPLYlink written 3.4 years ago by support50

support = aeinsights immo....

ADD REPLYlink written 3.4 years ago by apelin20470
1
gravatar for Vivek
4.7 years ago by
Vivek2.3k
Denmark
Vivek2.3k wrote:

I use pubmed on mobile sometimes. Other than that may be querying population frequencies for a mutation locus might be useful but otherwise I can't think of much else I'd want to check on my mobile.

ADD COMMENTlink written 4.7 years ago by Vivek2.3k
0
gravatar for aeinsights
3.4 years ago by
aeinsights20
aeinsights20 wrote:

Guys, It's great to see lots and lots of interest from the people over for mobile app. We build a platform that will enable quick view of your data with alters and notifications. Please visit bioelm.com for more info.

Thanks,

ADD COMMENTlink written 3.4 years ago by aeinsights20
5

"Lots and lots of interest"? Are you and I reading the same text?

ADD REPLYlink written 3.4 years ago by RamRS22k

FYI, bioelm.com doesn't work for me.

ADD REPLYlink written 3.4 years ago by Daniel3.7k

http://bioelm.com/ It works. Please check otherwise please share the screenshot.

ADD REPLYlink written 3.4 years ago by aeinsights20
1

It appears to be blocked within my university network (chrome & firefox on desktop, chrome on mobile via eduroam) but works on mobile chrome when disconnected from eduroam. Don't know if that is of importance.

ADD REPLYlink written 3.4 years ago by Daniel3.7k

Thanks Daniel... Glad you put an effort to view our site. We are open to host one of your data with visualization if you want for free. Thanks.

ADD REPLYlink written 3.4 years ago by aeinsights20

It was the same here. I'm guessing server location has some role to play?

ADD REPLYlink written 3.4 years ago by RamRS22k
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