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  • CWLEXEC: Run Common Workflow Language on HPC with IBM Spectrum LSF

    28 February 2018

    CWLEXEC: Run Common Workflow Language on HPC with IBM Spectrum LSF The [Common Workflow Language (CWL)]( is a community-led specification for describing analysis _workflows_ and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and _high performance computing_ (HPC) environments. [IBM Spectrum LSF]( (formerly IBM Platform LSF) is a complete workload management solution for demanding HPC environments. Featuring intelligent, policy-driven scheduling, it helps organizations accelerate research and design while controlling costs through superior resource utilization. Recognizing the popularity of CWL among LSF users, we introduce a new open source project **CWLEXEC** to support running CWL workflows on LSF. The project will feature smooth integration with LSF with high efficiency and scalability, self-healing of workflows, support user-specified submission options while keeping CWL definitions portable, and other benefits. * **Title**: CWLEXEC: A new open source tool to run CWL workflows on LSF * **Presenter:** Qingda Wang, Principal Architect, IBM Spectrum LSF Family Products and OEM * **Time**: 2018-02-28 14:00 GMT / 15:00 CET 2018-02-28 14:00:00 UTC 2018-02-28 15:00:00 UTC BioExcel Bioinformatics Genomics Workflows University of ManchesterBioExcel CoE Stian Soiland-Reyes [] bioinformaticiansHPC users workshops_and_courses registration_of_interest WorkflowsCWLHPCLSF
  • Open Life Science

    1 January - 22 April 2020

    Open Life Science The Open Life Science program helps **early stage researchers and potential academic leaders** in becoming **Open Science ambassadors**. Any questions? We are here to help - feel free to email []( or connect with us on Twitter [@openlifesci]( ## About This is a **15-week long personal mentorship and cohort-based training**, where participants (organisers, hosts, mentors and mentees) of this program will: - share their expertise and gain knowledge essential to create, lead, and sustain an Open Science project - connect with members across different projects, communities, backgrounds, and identities - empower each other to become effective Open Science ambassadors in their communities We are recruiting for our first cohort of mentees for the first round that starts in January 2020. We are also inviting mentors, experts and content developers to join us in shaping this program. ## Projects Participants will join this program with a project that they either are already working on or want to develop during this program. Your project ideas can range from solving technical questions, to creating an open data project or report, developing open source software project, writing open publication, facilitating community/team culture movements, advancing open educational resource or contributing to other existing projects/community. All applications are welcome, whether your project is just an idea at this stage, or something that is running for years, but, your projects must: - promote one or several [Open Science practices]( (i.e. Open Access, Open Source, Citizen Science, ) in life science - state a possible measurable outcome (i.e. feature, module, or minimum viable product) from this program - create an inclusive space and welcome contributions from their community members ### Why focus on life science? Modern life science and related communities stand in the interface of computational and biological research. This position provides an exciting opportunity for new scientists to understand and welcome "open by design" practices. We understand that our curriculum is applicable to various fields, but we want to focus on life science community/projects with this program due to an urgent need to promote open practices in this field. If you have a project idea that is not directly related to life science, we will ask you to describe how you aim to advance openness in life science through your work. ### What's in it for you? We want to make this program mutually beneficial for all the participants. Here are a few values we think you will receive from participating in this project. - Become a contributing member of this community - Collaborate with others in Open Science projects - Exchange skills with others and build your own profiles - Highlight and promote your resources - Gain insights from other experts in the field - Work on a short-term projects and publish online - Get recognition and acknowledgement for your work - Co-develop this program by sharing feedback ## Timeline ## The program itself *To illustrate the program, we will share the persona/story of Joy, a mentee participating in the program, and Sam, their personal mentor, as they progress through their open science journey.* In their applications, they will indicate their interests in the topics related to Open Science in bioinformatics. Joy will provide a short outline of their project, and Sam will list their expertise that they want to share with their mentee. After the selection process, they will be involved in the following steps of this program: 1. Based on their common interests, they will be introduced to each other as suitable mentee and mentor They will meet every 2 weeks. In these **mentee-mentor calls** (around 30 minutes), Sam will help Joy evaluate their understanding of the new topics, and review their progress by providing constructive feedback. Joy will be given relevant exercises before these calls to help them apply new skills in their project. When needed, Joy and Sam will be able to connect with other [experts](about#experts) and get consulted on their project. 2. Joy will participate to online calls where relevant contents related to Open Life Science is shared and discussed with all participants of the program. In these **cohort calls**, the program leaders will introduce new topics and resources, facilitate break-out discussions, and invite experts from the field to give talks. In the first call Joy will get to know all the participants of the program, present their project, learn about others' projects. A final cohort call will allow Joy to present their project to other participants and exchange values. 3. Sam will participate to **mentoring training** with topic-based discussions with other mentors aimed at enhancing their mentoring skills. After the 15 weeks of the program, a self-evaluation survey will help Joy and Sam in positioning their knowledge in open science leadership before and after the program. For the next round, Joy may share what they learnt by mentoring a project and Sam continue their mentor effort and/or become an expert ## Applications This program will focus on Open Science in the life sciences and bioinformatics domains. We are particularly keen to connect with the participants from less-represented European countries such as Hungary, Greece, Estonia, and Cyprus. We also invite applicants from outside Europe, particularly from developing countries (e.g. India and Africa - who are also timezone-compatible). Cohort calls will be conducted in English. However, our participants who have different primary languages such as Spanish, French, German, Hindi, and Portuguese, will be paired with mentors who can communicate in their preferred languages. 2020-01-01 09:00:00 UTC 2020-04-22 17:00:00 UTC Open Life Science Bioinformatics Biology [] [] PhD studentsLife Science ResearchersBioinformaticians and wet-lab biologistsresearch software engineers and research data managers working with ELIXIR-supported tools and resources workshops_and_courses registration_of_interest openlifesciolsopen sourceopen accessOpen scienceopen datapreprints

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