https://dokuwiki.computational.bio.uni-giessen.de/ 2026-05-06T10:59:25+00:00 https://dokuwiki.computational.bio.uni-giessen.de/ https://dokuwiki.computational.bio.uni-giessen.de/_media/wiki:dokuwiki.svg text/html 2017-09-07T14:21:37+00:00 Anonymous (anonymous@undisclosed.example.com) https://dokuwiki.computational.bio.uni-giessen.de/cloud:access?rev=1504794097&do=diff All access to the de.NBI cloud is secured by user credentials. Details depend on your affiliation: Affiliation Domain Username & password members of the computational bio group cb your UNIX login credentials external users with BCF UNIX account text/html 2018-02-28T15:35:30+00:00 Anonymous (anonymous@undisclosed.example.com) https://dokuwiki.computational.bio.uni-giessen.de/cloud:cider?rev=1519832130&do=diff CIDER The cloud file up- and downloader. Due to access restrictions of the object storage, submitting data is a cumbersome procedure for external collaboration partners (subsequently denoted as data sender, DS). Moreover, the bioinformatician (subsequently denoted as data receiver, DR), is often involved in multiple projects at the same time and hence would like to keep track of who has submitted which data to which destination. To achieve the latter, CIDER has been developed as a user friendl… text/html 2017-05-22T14:24:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://dokuwiki.computational.bio.uni-giessen.de/cloud:concepts?rev=1495463066&do=diff Cloud concepts: Domain, User, Project, Role, Image, Flavor, Network, Instance, Volume, Key pairs Before using the cloud, a user needs to be familar with certain concepts. Most of these concepts are applicable to almost all clouds (openstack based private clouds, Amazon EC2, Microsoft Azure text/html 2017-09-15T11:14:23+00:00 Anonymous (anonymous@undisclosed.example.com) https://dokuwiki.computational.bio.uni-giessen.de/cloud:custom_images?rev=1505474063&do=diff Custom images Introduction To simplify usage of the de.NBI cloud custom images are provided. These images contain an operating system (OS) and preinstalled software/tools required for different bioinformatic applications. By launching a virtual machine (VM) based on a custom image, specific bioinformatic analyses can be performed without having to take care of installation procedures. text/html 2018-07-06T13:45:23+00:00 Anonymous (anonymous@undisclosed.example.com) https://dokuwiki.computational.bio.uni-giessen.de/cloud:first_steps?rev=1530884723&do=diff FIXME Guide for old cloud Introduction As computational power highly depends on sufficient hardware resources, it is a matter of financial liquidity and adequate premises whether enough computing capacities can be supplied. Hence a central facility is desirable which pools monetary efforts and provide a de facto computational platform for bioinformaticians and life scientists (henceforth called users) in the field of microbiology. In Giessen, the Bioinformatics Core Facility (BCF) provides and… text/html 2017-09-12T11:11:01+00:00 Anonymous (anonymous@undisclosed.example.com) https://dokuwiki.computational.bio.uni-giessen.de/cloud:flavors?rev=1505214661&do=diff Available Cloud flavors Based on our hardware setup we provide the following default flavors that can be requested for running an image: de.NBI default: 2 VCPUs, 2 GB RAM This is the default flavor that can be used for running simple command line applications and for testing purposes. text/html 2018-03-08T14:31:03+00:00 Anonymous (anonymous@undisclosed.example.com) https://dokuwiki.computational.bio.uni-giessen.de/cloud:gitlab-runner?rev=1520519463&do=diff Example Installation of a gitlab runner * Create a Ubuntu VM (it does not need a floating IP) * Connect to your VM * curl -L https://packages.gitlab.com/install/repositories/runner/gitlab-runner/script.deb.sh |\ sudo bash * sudo apt-get install gitlab-runner text/html 2017-05-22T14:24:25+00:00 Anonymous (anonymous@undisclosed.example.com) https://dokuwiki.computational.bio.uni-giessen.de/cloud:image_builder?rev=1495463065&do=diff Diskimage Builder Installing Diskimage Builder Github diskimage-builder repo Openstack diskimage-builder user install guide First, update your system as root: $ apt-get update $ apt-get upgrade To install the diskimage-builder on your instance, you need pip. Run as root $ apt-get install python-pip After this, install the text/html 2017-09-15T16:59:27+00:00 Anonymous (anonymous@undisclosed.example.com) https://dokuwiki.computational.bio.uni-giessen.de/cloud:images?rev=1505494767&do=diff Using and managing images Introduction To start a virtual machine in Openstack a virtual machine image (brief: image) is required. Images are files that contain a bootable operating system. Cloud images are available for various operating systems like Ubuntu or CentOS. They are usually separated from the normal installation images. For Ubuntu and CentOS7 the cloud images can be found here: text/html 2018-07-09T14:19:45+00:00 Anonymous (anonymous@undisclosed.example.com) https://dokuwiki.computational.bio.uni-giessen.de/cloud:index?rev=1531145985&do=diff The de.NBI Cloud at Giessen University In 2016, Justus-Liebig-University Giessen (JLU) was selected as one of the five hosting sites of the de.NBI Cloud to provide scalable storage and compute resources to researchers in the bioinformatics community. The OpenStack based cloud computing infrastructure is managed and administrated by the Bioinformatics Core Facility (BCF) at JLU. Since June 2017 the initial setup is in production mode based on dedicated BMBF funded hardware. Access is granted bas… text/html 2017-05-22T14:24:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://dokuwiki.computational.bio.uni-giessen.de/cloud:juju?rev=1495463066&do=diff JuJu JuJu is an orchestration tool developed by Canonical. By utilizing JuJu it's possible to deploy and represent services from bare-metal (e.g. OpenStack) to application level (e.g. Owncloud), hence JuJu operates on the three major cloud service models: PaaS (Platform as a Service), IaaS (Infrastructure as a Service) and SaaS (Software as a Sevice). These services can be modeled and scaled not only using the comprehensive command line interface (CLI), but also by a ready-to-use graphical user… text/html 2017-09-18T17:23:06+00:00 Anonymous (anonymous@undisclosed.example.com) https://dokuwiki.computational.bio.uni-giessen.de/cloud:network?rev=1505755386&do=diff Networking Introdcution Openstacks networking component is called Neutron. During the first steps of the quickstart guide it is shown how to build up a network using a single VM. This section will give some brief background information on openstack networking as well as some suggestions regarding the openstack installation in Giessen. Some of the details described in the following are shortened for the purpose of simplicity and better understanding. If you want and or need to get a deep unders… text/html 2021-03-03T07:47:50+00:00 Anonymous (anonymous@undisclosed.example.com) https://dokuwiki.computational.bio.uni-giessen.de/cloud:object_storage?rev=1614757670&do=diff S3/Swift object storage in the de.NBI Cloud Introduction Object storage is a type of storage to store and share data in cloud environments. An object consists of a unique name, the actual data and associated metadata (like access restrictions and user defined metadata). Contrary to filesystems objects are not organised in a hierarchy, but in a flat container. The data is accessed via http based protocols/APIs (application programming interfaces), like s3 and swift. text/html 2017-05-22T14:24:25+00:00 Anonymous (anonymous@undisclosed.example.com) https://dokuwiki.computational.bio.uni-giessen.de/cloud:openstack?rev=1495463065&do=diff OpenStack basics OpenStack is a free and open-source software platform for cloud computing, mostly deployed as an infrastructure-as-a-service (IaaS). The software platform consists of interrelated components that control diverse, multi-vendor hardware pools of processing, storage, and networking resources throughout a data center. Users either manage it through a web-based dashboard, through command-line tools, or through a RESTful text/html 2017-05-22T14:24:25+00:00 Anonymous (anonymous@undisclosed.example.com) https://dokuwiki.computational.bio.uni-giessen.de/cloud:orchestration?rev=1495463065&do=diff Orchestration of services and tools in a Cloud Computing environment Besides using a single VM running separately in a Cloud infrastructure specialised orchestration frameworks can be used to start a variety of services (e.g. file server, database server) or even a larger number of identical computing nodes in a synchronised manner automatically. text/html 2017-10-05T13:12:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://dokuwiki.computational.bio.uni-giessen.de/cloud:quickstart?rev=1507209132&do=diff This is the quickstart to start your own running virtual maschine in the de.NBI cloud. To start this guide you should have an individual account and be a member of an existing project. If you do not have an account, please visit this page and follow the instructions. text/html 2017-09-15T11:57:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://dokuwiki.computational.bio.uni-giessen.de/cloud:security?rev=1505476666&do=diff Security aspects in clouds One important change triggered by the rise of clouds is a shift in responsibility. In the pre-cloud world, a system administrator was responsible for taking care of system, installing security patches and fixes, securing the network, settings up firewalls and monitor the operation state of servers. text/html 2017-09-12T11:25:17+00:00 Anonymous (anonymous@undisclosed.example.com) https://dokuwiki.computational.bio.uni-giessen.de/cloud:volumes?rev=1505215517&do=diff Volumes in the de.NBI Cloud Volumes are durable data storage devices which can be attached to virtual machines (VM). Just like for example portable hard drives they can only be attached to one VM at the same time. Nevertheless, volumes can be attached, detached and reattached as often as desired. Thus, volumes can be used to persistently store data and transfer it between different VMs.