Newsletter May 2018

Dear All,
this is an a-periodic communication concerning the bioinformatics activities of the BIOINforMA (Bioinformatics for Marine biology) project.
With this update we mean to keep you informed on the start-up, and current developments and settings of the services.
We will also let you know about upcoming events concerning bioinformatics.
We apologyze with those that are not interested in the subject.


  • BIOINforMA is organizing services and tools expected by the end of this years, and is pursuing the scientific goals of the Bandiera Project that supports the start up. However, we are already trying to offer support on specific efforts in collaboration. This is helping to appropriately consider all main issues and needs that can be of general interest in the institute, although we are still focused on the internal training and set up period.
  • BIOINforMA website
    Check out our website! Comments and suggestions are always welcome. The website will be updated on a regular basis with tools, news and events.
  • In the Services -> Software section of the website a list of software and tools already available on the SZN cluster is provided.
    If you are an expert UNIX user you can ask for a login and password to use the Cluster through the ticketing system.
    For those that are not expert, we are organizing web-based services or we will support the analysis meanwhile the web tools will be finalized.
  • Ticketing system
    As announced during Chiusano’s introductory seminar, the ticketing system is running since a while! You can access using your mailbox credentials (e.g. as username).The ticketing system is the unique entry point for EVERY request you need to submit to the BIOINforMA Service:

– asking for technical assistance;
– requesting access to resources;
– asking for software installation on the SZN cluster;
– asking for consulting;

all are tasks that can be efficiently requested using the ticketing tool.
Please note that our policy from now on will be to refuse any request not following this system, since this is an objective first in first out system that will help us to trace our priorities and report the state of the art for all the activities.
So please avoid the phone calls to ask for help and start getting familiar with this system. If you will have problems, people from the BIOINforMA service will help you in opening your ticket. When you will open your ticket, you will receive timely feedback and indication on the status of your request.
Indeed, through this system, you will be able to track its completion status step by step via the web interface.

  • Gitlab platform (for expert users):
    Gitlab is an open source platform acting as a code versioning system (github like) using the popular “git” software as a backend. Last year we deployed an internal instance of this tool to manage all the code
    developed internally in SZN. We are sure that if you are into code development you will absolutely love it!
  • BlastServer:
    Using bleeding edge container technologies, we are now able to deploy web based blast services with your desired dataset(s) or reference database(s). The service is being set up, it is currently experimental and could undergo improvements in the next months, but you are very welcome to ask for it soon. Limits are depending on computational power and disk space.
    To set up a BLAST service using your data as a reference database, you should carefully and appropriately organize your collections in a fasta format with proper IDs.
    Follow the instruction in the module of request for BLAST services, think what you need to do and fill the mandatory information. Then send it to attaching the signed module. You will receive feedback in short from your request.
  • Hardware sharing and care:
    Please note that we have not personal enough to take care of your unix machine. We only can consider a server or a cluster in case you want this machine to be part of the SZN scientific computing facilities under care of the BIOINforMA expert unix systems administrator. To this aim, you need to contact us to define if this is possible in the specific moment of your request (limits may be of space in the cluster room and
    of personnel to take care of the single machine). Your machine should be moved in the cluster room, in case.
    We hope you may understand that this service is valid only for servers, clusters and big workstations for scientific research, and this is offered with the aim to centralize the SZN scientific computational power.
    Of course rules and roles must be agreed. In these specific cases, send an email to attaching the hardware request module to evaluate your specific needs. Please fill all the mandatory information, sign and send it.
  • NOVEL tools:
    Please visit our site in the section Services/Bioinformatics Platforms. You may find some active services:
    We are now releasing GLOSSary, a platform where you can visit and BLAST our collection of 16S sequences obtained by a novel processing of the TARA collection.
    You will find the user guide on the main website.
  • Expected courses from BIOINforMA:
    Introduction to Bioinformatics and BIOINforMA services
    DATE to be announced


Sincerely yours,
The BIOINforMA group

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