Goal: help the drosophila community

Welcome to Drososhare’s Blog! Drososhare.net is still in development, but I want to share my enthusiasm with you. In this first blog entry, I would like to explain how Drososhare will help us, drosophilists. Let’s start with a short Success Story:

A couple of months before I wrote this in 2014, I got an e-mail from a student of a fellow German lab and the next day, I received an e-mail from her boss, with a similar content : Have you received the UAS-Tdc2-RNAi fly line already? We have received it from Bloomington, but all flies were dead. We urgently need this fly line. So if you have it, I could drive to Berlin and pick it up. Would that be possible?”. You probably understand the urge, as I did. I was on holiday, but fortunately got to read my e-mails on that day. I forwarded that one to the PhD student (who was -oh surprise!- not on holiday). They had just received a healthy batch of these RNAi flies and could send it to them. The flies arrived two days later and the student could do her experiment: Science could go forward.

This image shows a 0.1 x 0.03 inch (2.5 x 0.8 ...

If you can’t tell it’s a male, Drososhare will probably not be for you. (Photo credit: Wikipedia)

What a nice story, isn’t it? It is unfortunately only one happy end in a sea of tragedies implying flies dying during transport or killed at the customs. Fly sharing between labs does not always go so smoothly either. Tell me about imprecise or wrong batch labeling. Tell me about the hours spent writing e-mails to get the label translated. Tell me about these red-eyed Cyo flies labeled “w- control+ (III)”…

With Drososhare, these common problems will become the exception, and the success story will become the rule. The solution looks simple: to gather information about which fly stocks are kept in which lab. As simple as having one mutant cell in an otherwise wild type individual! The comparison with the MARCM technique can be taken further: A great simple idea, followed by a long and difficult development, and ending with an easily usable tool (we could add that the tool is first available for Drosophila only, but let’s stop making other biologists jealous). Drososhare  provides a technical solution to collect and redistribute your stock list information, in an easy manageable and safe way. Our aim is to tighten the drosophila community even stronger. Stock centers have been doing a great job for 100 years (happy birthday BDSC), but their centralized nature have some limitations. We will centralize the information, but fly stocks will remain distributed: Drososhare is a distributed stock center.

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Fly hunter for hire !

Difficulties in sourcing a Drosophila fly stock?
I, Dr. Julien Colomb, will track it down for you.

wantedposter

Give it a try. You tell me what you need, I propose flies to order and you decide which one you want: I will make sure you get the flies and a good description. We are launching this personalized service, the pricing is super attractive: (pricing valid in June 2017):

  • 2 € per stock listed in flybase.
  • 4€ per NIG stock not in flybase.
  • 50 € per stock not found in stock centers.

For example, to the query “get me all RNAi lines against apterous”, I would propose:

2€ y[1] v[1]; P{y[+t7.7] v[+t1.8]=TRiP.JF02311}attP2
2€ y[1] sc[*] v[1]; P{y[+t7.7] v[+t1.8]=TRiP.HMS02207}attP2
4€ ap.RNAi_NIG/TRip_8376R-1
4€ ap.RNAi_NIG/TRip_8376R-2
2€ P{KK108926}
50€ P{GD4675} (not in VDRC anymore)

 

To hire me, send me an email at: julien [at] drososhare.net

Providing Drosophila through Drososhare: save time and gain reputation

You feel you spend too much time sending flies to the community or you would like that work to be recognized? Use Drososhare! And:

  • Decrease the number of fly requests.
  • Decrease the time required per fly request
  • Gain visible reputation
  • Get a discount on future purchase.

Providing your flies through Drososhare is free and require little efforts, i.e. get a drososhare account and upload a list of flies you are willing to share with the community. We can assure you that both the amount of fly requests you will receive (1) and the amount of time spent on each request (2) will decrease. In addition, we will track both the amount and the quality of your work as a fly provider and will provide you with a summary of your lab’s achievements (3, in construction, feedback welcome). In addition, you will get a discount on future purchase (4), for each stock you send.

1. Decrease the number of fly requests.

Each time a lab request a fly line via Drososhare, the flies will be automatically added to their Drososhare stock list. While it will make it easier for that that lab to report the correct name of the flies and correct reference in future publications, it will, and that’s probably the most important, makes that lab a putative source for that fly line. This means that next time a lab is requesting this stock on Drososhare, the request may be directed to a different lab. The amount of request to your lab for this line will decrease exponentially, since the work is distributed between drososhare users.

Of course, this means that your lab will also become a source for flies you will order on Drososhare. In order to assure you that the number of requests will never exceed your capacity to send flies, we integrated a tool to set the maximum number of orders you will accept per month.

2. Decrease the time required per fly request

For the PI

You might not do much, but forwarding emails at the moment? It won’t change much in that case, but you will get less emails, since some users will know about drososhare.

Instead of forwarding the email, reply to it with a predefined message (that can be saved as a signature, for example): “Thank you for your request, we provide these flies through the Drososhare service. Forward this email to info@drososhare.net and an account will be made for you and your lab. You will receive a password and further information shortly afterwards. Please order flies via the platform and we will be happy to send you the flies you need, if we have it.”.

For the lab members

The work of the person dealing with the request itself will be highly reduced. While so far, he had to:

  • Make sense of the request (the name used in the request in often not the one you will find on the fly stock list)
  • Locate the flies in the lab
  • Write new labels and the address of the requesting lab
  • Send the box with the flies
  • Do all of it for each email received.

With Drososhare, most of the work will be done by the requesting lab or automated by the platform. The work is reduced to:

  • accept the orders (rapidly check that the fly requesting the lab made no mistake in their request),
  • download and print the list of all formatted requests (address of the recipient, name of the flies and their location in the lab)
  • process all request (coming form different labs) in one go.

3. Gain visible reputation

Since we are saving some data for each transaction, we will be able to deliver some statistics about your activities as a fly provider, for instance:

  • How many flies you have shared with the community
  • Statistics on delivery time
  • How many labs are using flies originally coming from your lab

Whether we will create web pages for each lab, widgets to incorporate on your website, or another form of visible reputation label is still unclear. Any suggestion is welcome!

4. Get a discount on future purchase.

Ordering flies in fellow labs cost 7€ per line (there is no extra fee for ordering from stock centers).  For 5 stock sent to a fellow labs, you will receive 2 free orders, i.e. for each fly send, you get a discount of 2.8 € (Price 2017).


Get a drososhare account and start saving time!

Still not convinced? Please tell us why!

Our wish for 2017: a clean stock list for your lab.

Unlike “doing sport” or “quit smoking”, the wish “Finally, get this fly stock list cleaned” might be a one time only wish. What about working with us and get your list cleaning itself? Is this even possible ?

As a open data advocate, I am eager to tell whoever want to listen that tidying up data is an investment that pays off: you will get more efficient and opening up your data will become possible and easy. Getting your data organized is a skill every scientist should learn! I think this is also the case for lab material, fly stocks included.tidyup

Tidying up the stock list will probably be a long process, and splitting it in several easier steps might be an efficient strategy. First we need to make sure that once cleaned, the list will stay clean: we will prevent the entry of bad data. Then, we will get to the other steps: tidy your list format, label your clean entries, modify the entries which are not clean, find a way for that information to end up in your papers.

1. Allow only clean NEW ENTRIES

A. The manual way: When you get new flies, make sure to enter their rightful name, as presented on flybase, along with the flybase number of the stock (prefer this to the stock center number, it should start with FBst….). If the stock has no flybase number, get the FB ID of the interesting genetic element, prefer the insertion ID (FBti) to the transposon ID (FBtp). Be sure the whole lab is doing so, and that the information is kept in one update, safe document. Also add dates of order and provenance of the flies.

B. The easy way: Push the red button you find  here.

and send the email to your lab keeping us in CC. We will register your lab in Drososhare and your lab can pre-order your flies on our platform. Ordered flies will be automatically added to your Drososare stock list. You can later download your stock list with clean information anytime. No fee applied for this function.

2. Get a tidy list format

A. The manual way: make sure you have one unique header line, one row is one fly line and each fly line has one unique row, one sheet for the whole lab, save as a .csv file (only text, no color code for example).

B. The easy way: none yet.

3-6  …

For the following steps, I will build an open source R shiny application to get an easy workflow, and modify this blog post along the process. If you wanna help me with that, please go to: https://github.com/jcolomb/flystockcleaner.  The current version (https://colomb.shinyapps.io/Flystockcleaner/) can transform BDSC number and flybase stock numbers into stock names (plain text and with link to flybase alleles, as on flybase).

Screen Shot 2017-06-27 at 01.51.46

Dr. Julien Colomb

One unique basket for all fly orders !

Time to buy some fly lines?
Use the free drososhare system:

* One basket for all lab members
* One basket for all stock centers
* Ordered flies automatically added to your stock list.

Click here and get started: it will open an email for you to send to your lab mate

(keep us in the recipient list of the email and we will create/update your lab account such that every lab member can start putting flies in your shopping basket.)


Happy Advent time !

Here are a bit more background on this new feature of Drososhare.
While the ultimate goal of Drososhare is to facilitate lab-lab fly transactions and help the community, we realized that the system has also advantages when ordering flies from stock centers. In particular, we designed the platform to have one shopping basket for the whole lab, and we have now extended our database, such that this basket can include flies from the 4 major stock centers (Bloomington, Vienna, Kyoto and NIG) as well as participating labs. This makes Drososhare a nice shopping platform designed for drosophila labs!

For each Drosophila lab, Drososhare now offers a way to organize the fly orders:

* Every lab member can add flies into the lab basket
* The lab admin send a grouped order.
* Orders are then transferred to the different stock centers. *

Bonus

* Ordered flies information is included into your drososhare stock list, automatically
* Easily spot stock center flies via their status
* It is free *

Get it started and push the red button above to send an email to your collaborators (keep us in the recipient list). We will create an account for each recipient and your whole lab can start preparing their shopping list!

Note that if you opt for becoming providers of flies to the community, you will automatically become a provider for flies you order from fellow labs (stock centers prevent redistribution).

I hope you will enjoy your next fly order, if you have any question, simply send me an email.

Sincerely yours,
Julien Colomb
CEO Drososhare

Available sources for flies (the 12/05/16):

Bloomington Stock center
Kyoto Stock center
NGI Stock center
VDRC
2 participating labs
(Other Stock center will be incorporated soon)

139 084 fly lines in the database

Preorders from different lab members will be listed in your preorder page.

* There is no additional fee when ordering from stock centres. The system works only semi-automatically at the moment, but we will contact stock centers to make the process even smoother in the future. We make money when you order flies from fellow labs who agreed to provide flies for the community.  https://drososhare.wordpress.com/

Stock search: tips and tricks

See the video for an initial process walk-through.

Notes:
FB stands for flybase

  • Bloomington flies have their FB number in prefix.
  • Sometimes FB names and bloomington names do not fit perfectly, if you cannot find the stock with its name in FB, use the FB number (Fbst00xxxxx).

  • For RNAi search, try also ‘genename’.RNAi since we modified the NIG fly name to fit that description. Note that NIG Stock center is not in FB and that some NIG flies are in Bloomington (under a different name).

 

  • If “Status” in the result is “stockcenter”, these flies will come from a stock center (ordering them will cost you the stock center fee). Any other status would mean that the flies are in a fly lab (the name might be identical, ordering them cost 7€ per line).
  • You can use the “go back” button of your browser to change the search.

 

  • Sorry for the non-optimal visualisation of the results and the bugs in search with elements not in FB (see last 3 min. of the video).
  • note that the bug in search with elements not in FB does not appear if you search for more than 1 element and that one of the searched element is in FB.

Let’s mirror the Bloomington Drosophila stock center, NO extra work NO extra funding ?!

Order your flies via http://www.drososhare.net and the BDSC will be mirrored by the end of 2017 in Europe.

bdsc                flowRoot3097.png

 


Dear Drosophilists,

Are you annoyed with the long delivery time of the Bloomington stock center?
Did you already got flies killed at the border?

You dream about having a huge Drosophila stock center in your country? Then stop dreaming, purchase your flies through Drososhare and let’s make it a reality!

My name is Dr. Julien Colomb, I am a neurobiologist (http://orcid.org/0000-0002-3127-5520), leader of the Drososhare project. With my team, we’re passionate about making Drosophila research more efficient. Drososhare is linking your fly inventory with your fly purchase (the benefits of this link are numerous and will be detailed in further posts). In addition, it transforms your lab into a source of flies for the community.

How does it work ?

Every member of your lab choose flies to order on the Drososhare platform and the PI sent the order. Fly requests are then forwarded to either the Bloomington stock center or the Kyoto Stock center; while the fly description is automatically added to your (safe and secret) Drososhare stock list.

Next time a fellow scientist look for that stock, we may forward his request to you (if you opt for it). You have become a mirror for that stock in your country. Since most flies available at the BDSC are sent once a year in Europe, we could get all of them in the Drososhare database at the end of the year, without extra work.

Where is the catch?

There is no additional fee when you order flies in stock centers. However, for every Peer to Peer transaction, we will charge the lab requesting the flies 7€, and give a discount to the providing lab: 2 free orders for 5 stocks sent (Pricing 2016-2017).

Other main benefits

  • The order system of Drososhare works with a basket. Any lab member can add pre-orders to the basket and you can bundle them into one order very easily. It saves trouble, time and money.
  • If you upload your current stock list, you can keep your inventory in one place.
    • You can mark any of your current stock as “public” and make them available to the community (including flies absent from stock centers !).
    • Since our search function is looking for synonyms, you do not have to clean your stock list for the flies to be findable.
    • Fly requests are sent directly to the TA, not bothering the lab PI.
  • Your stock list is getting cleaner with every purchase.

So, let’s strengthen the Drosophila community together.
Signal your interest at julien@drososhare.net, and please comment below.

Sincerely yours,

Dr. Julien Colomb
http://orcid.org/0000-0002-3127-5520
julien@drososhare.net