Workshops & Tutorials
Links in this page: Two Day Workshops | Galaxy Africa | Machine Learning & Omics Data
One Day Workshops | New Features of the UCSC Genome Browser | Resources for Mining & Interrogating Large-scale (Genomic and) Epidemiological Datasets | Resources and Tools for Computer-Aided Drug Discovery | H3BioNet
Two Day Workshops
Galaxy Africa 2019
14-15 November
Description
GalaxyAfrica 2019: After a successful GalaxyAfrica2018 in South Africa, we are pleased to announce the next GalaxyAfrica workshop in collaboration with the ASBCB/ISCB Africa conference in Kumasi, Ghana. Building on the previous event, we will offer Galaxy training for researchers, and training for systems administrators who need to maintain a local installation. This year we are calling for abstracts for three oral presentations that demonstrate the use of Galaxy in your research projects.
Participants will NOT need to bring their own computers as the room provides them but you may bring your own device if preferred.
Intended audience and level
Galaxy Africa will target 2 audience groups:
- Those aiming to do bioinformatics on the Galaxy platform. The content for this group will be aimed at an introductory level for prospective bioinformaticians.
- Those intending to run Galaxy as a service for their bioinformatics users. The audience here is systems administrators for bioinformatics facilities.
Machine Learning & Omics Data: Opportunities for Advancing Biomedical Data Analysis
14-15 November
Description
Machine learning has emerged as a discipline that enables computers to assist humans in making sense of large and complex data sets. With the drop in cost of sequencing technologies, large amounts of omics data are being generated and made accessible to researchers. Analyzing these complex high volume data is not trivial and the use of classical tools can not explore their full potential. Machine learning can thus be very useful in mining large omics datasets to uncover new insights that can advance the field of medicine and improve health care. The aim of this tutorial is to introduce participants to the Machine learning (ML) taxonomy and common machine learning algorithms, as well as the necessary concepts related to the experimental design. The tutorial will cover the methods being used to analyze different omics data sets by providing a practical context through the use of basic but widely used R and Python libraries. The workshop will comprise a number of hands on exercises and challenges, where the participants will acquire a first understanding of the standard ML processes as well as the practical skills in applying them on familiar problems and publically available real-world data sets.
Participants will need to bring their own computers.
Intended audience and level
This tutorial is aimed towards novices (no prior knowledge / expectations in NGS data analysis or Machine learning). However, participants should be somewhat familiar with:
- R (base commands)
- Unix shell (running basic commands)
Participants should bring their own laptops for the practical exercises.
One Day Workshops
New Features of the UCSC Genome Browser
14 November
Description
The UCSC Genome Browser workshop will be a one-day experience consisting of a half day of presentation showing the latest tools and features of this large and complicated online software package. The afternoon session will be hands-on problem solving to solidify the learning and offer opportunity to discuss participant-generated questions. Specifically, the new data types, interact and barChart, available for user-generated custom tracks will be presented, as will the very new Genome Browser API.
Participants will NOT need to bring their own computers as the room provides them but you may bring your own device if preferred.
Intended audience and level
The session is for bioinformatics professionals and students and molecular biologists, typically at the graduate student level or above. Participants should have considerable background in Molecular Biology and Genomics and at least a basic understanding of databases. Some previous familiarity with the Genome Browser will be useful. The session should be considered intermediate in difficulty. The session should be considered Intermediate in molecular biology expertise and Introductory/Intermediate in bioinformatics/programming/genomics.
Resources for Mining & Interrogating Large-Scale (Genomic and) Epidemiological Datasets
14 November
Description
EuPathDB.org is a free, online resource intended to empower investigators with tools/materials necessary to interrogate data associated with global infectious disease. This workshop will introduce users to ClinEpiDB.org focusing on clinical and epidemiological datasets. the majority of sessions will be hands-on, facilitating understanding of foundational epidemiologic and exploratory data analysis concepts. Participants should have a basic understanding of epidemiologic research, data collection and data storage but ClinEpiDB is intended for novice data managers or analysts.
Participants will need to bring their own computers.
Intended audience and level
The ideal participant has a desire to become an expert user of ClinEpiDB, either as a biologist driven by infectious disease, public health or epidemiologic research questions, or as an informaticist interested in exploring available datasets with the potential to carry out novel analysis, or develop new analytical tools for broader distribution (perhaps in partnership with the EuPathgDB team). Attendees should have a basic understanding of epidemiologic research, data collection and data storage … but note that ClinEpiDB is intended for exploratory data analysis, rather than as a cutting-edge research tool for professional statisticians and epidemiologists.
Resources and Tools for Computer-Aided Drug Discovery
15 November
Description
Advances in computational technologies coupled with rapid growth in available chemical and genomic data provide multifaceted in silico approaches to the discovery of new bioactive compounds for diseases like tuberculosis, malaria, HIV etc that are burdening the world. Supported by the Wellcome Genome Campus Advanced Courses and Scientific Conferences, this introductory level workshop for Postgraduate students and researchers in life sciences, offers participants an overview of computational resources and tools, basic bioinformatics and chemoinformatics techniques used in the early stages of drug discovery as well as data retrieval from related databases. Activities will consist of presentations, demonstrations and practical activities to give participants hands - on exercises.
Participants will NOT need to bring their own computers as the room provides them but you may bring your own device if preferred.
Intended audience and Learning Outcomes
Postgraduate students and researchers in the life sciences (including the fields of computational biology/chemistry, chemistry, biology etc.). The material is considered introductory.
By the end of the course, participants will be able to:
- Describe the drug discovery pipeline and how computational methods are used to facilitate drug discovery and development.
- Apply homology modelling to calculate 3D protein structures.
- Retrieve and analyse protein and chemical data from databases such as Protein Data Bank (PDB), ChEMBL, ZINC and perform docking calculations.
Attendance is limited to 30. Participants are expected to bring their own laptops. The course will not cover programming.
H3ABioNet - Data Management Plans for
Grant Proposals & Research
15 November
Description
Research funding agencies are increasingly demanding the submission of a data management plan (DMP) as part of the application. A DMP serves as an instrument for managing the research data generated in a project. It describes what data to collect or generate in the course of the work and what should be done with it during the entire data lifecycle (eg storage, publication, citation, long-term availability, anonymization, reuse, etc.). The aim is to make not only publications but also research data findable, accessible, comprehensible and reusable. The availability of research data in the sense of open science can be ensured by data archives or repositories. Nevertheless, data protection and copyright aspects must also be considered.
The H3ABioNet workshop deals with the core elements of the DMP and introduces the single stages of the data life cycle from the perspective of bioinformatics and genomics research practice in human health and agriculture.
The workshop also discusses strategies for compatibility of the requirements of open science and data protection - such as anonymization, informed consent, licensing or access restrictions. In addition, useful data archives and repositories and their possible uses will also be presented.
Participants will need to bring their own computers.
Intended audience and level
This is an introductory session to data management plan aiming to help PhD students, Post-doctoral and early career researchers understand the DM process and how to write a good DMP to apply for grants and/or to organize their projects data. This workshop will also cover other aspects related to data management such as the process of making data FAIR and ethical aspects related to data sharing.
Special Session Submissions
ISCB-Africa ASBCB Conference features a Special Sessions track for emerging research areas. In its structure, each session(s) provides a more in-depth look at the subject matter presented. Proposals for special sessions should be submitted via the online submission system at https://www.iscb.org/submissions/index.php?id=257 by August 31, 2019.
Special Sessions have the purpose of introducing the ISCB community and conference delegates to relevant 'hot’ topics. Sessions can be considered as mini-symposia on timely topics, or new emerging area presented by top experts.
A wide range of topics is possible, as long as they are of relevance to computational biology and bioinformatics. We also encourage topics that are marginal to computational biology but clearly will need the involvement of such expertise in the near future. The proposed topics for Special Session might, for example, cover emerging themes the conference is not currently approaching with the desired proficiency. Some attractive topics include:
- Plant Biology
- Biomedical Data
- Agricultural bioinformatics
- Biomedical Ethics
- Drug design and discovery
- Text Mining
In addition we would like to encourage submissions that deal with the Society-Computational Biology interface. Examples might be “Genomic data sharing and privacy”, "Bringing genomic medicine to the clinic”. We encourage you to submit a proposal on an area that you deem as important to the computational biology community and may impact the future of the field.
Proposals should include the following details:
- Title (up to 20 words, preferably worded to pique delegates' interest)
- Topic: Describe the field to be covered by the session(s) and its relevance for conference participants (about one page)
- Meeting details
- Duration (no more than one hour)
- Expected sessions / topics, if possible with an explanatory paragraph about each
- A draft schedule showing how the sessions / topics will be organized including placement of keynotes, accepted talks, panel discussions, etc.
- How presentations will be selected (invitation, call for submissions, etc.)
- Possible speakers. This is not required, but may add weight to the proposal—indicate speakers who have already agreed to participate. NOTE: See Special Session Registration information for more details about compensation.
- Previous meetings of this with attendance statistics, if held before
- Potential sources of sponsorship for the session(s). ISCB provides session organizers with one-day complimentary registration for the invited speakers (maximum of two (2) per session) for those attending the conference for the sole purpose of presenting within the Special Session. We encourage the organizers to approach experts from related fields and communities that are not necessarily attending the conference routinely. Organizers will be responsible for raising sponsorship for additional complimentary registrations.
- Information about the organizers: full name (including title), affiliation, e-mail and postal addresses, telephone numbers (work and mobile, if available, including country and city codes), URL of home page, and qualifications to organize this meeting.
Special Session Registration
Organizers must identify the session speakers designated to receive the complimentary one-day registrations by September 15, 2019 by contacting This email address is being protected from spambots. You need JavaScript enabled to view it. in order to receive special registration instructions. Organizers and presenters within the Special Sessions are responsible for their own travel costs and if attending the full conference are responsible for the full conference registration fee. If needed, organizers are encouraged to seek sponsorships and/or use grant funds available to them to cover their own and their speakers' travel and registration costs.
Workshop & Tutorial Submissions
Links in this page: Proposals | Proposal Evaluation | Session Materials | Copyright | Compensation | Key Dates
This call is an open invitation to scientists and professionals working in the fields of bioinformatics and computational biology to submit high quality proposals for tutorials, workshops or mini-courses (tutorial program) at the ISCB-Africa ASBCB Conference 2019. Workshops will take place on November 14th and 15th.
The tutorial program provides participants with lectures and instruction covering either basic training for bioinformatics, well-established technologies/analyses or new "cutting-edge" topics relevant to bioinformatics and computational biology in Africa. The sessions should offer participants an opportunity to get an introduction to important established topics, to learn about new areas of research, or to develop advanced skills in areas about which they are already knowledgeable.
Tutorials may include any form of presentation such as talks, panel discussions or hands-on training. They serve an educational function and are expected to provide a balanced perspective on a field of research. Sessions on broadly used bioinformatics tools (Ensembl/UCSC, Galaxy, Cytoscape, etc.) will be considered.
Please note that if you wish present on a specific software package/method that is less widely used, your proposal should be submitted to the Technology Track. These presentations do not fall under this call for proposals.
Sessions should be designed as half-day (four hour), full-day (8 hours) or two-day (16 hours) sessions. (A 30-minute break is scheduled for morning and afternoon and a lunch break mid-day). Consideration for acceptance will only be given to proposals providing either:
•Direct practical, hands-on application of the subject matter
or
•Bringing together people with common interest for discussion
Proposals
Proposals should be submitted via the online form by 28 June 2019.
Proposals should contain the following information:
- Title
- Goals, objectives and motivation of the session
- Proposed Length of training course
- Half-day
- Full-day
- Two-days
- Detailed outline of the session agenda
- Please adhere to the page limit, but provide sufficient information for a thorough evaluation to be made.
- Intended audience and level
- It should be clearly and precisely indicated at whom the session is aimed, and at which level it would be taught with respect to the different underlying scientific fields. In particular if any background (biology, algorithmics, statistics, etc) is expected, this should be very precisely described.
- Where appropriate, indicate whether the material is considered Introductory, Intermediate or Advanced.
- Please indicate whether attendance should be restricted to limited number of participants
- Organizers & Presenters (where appropriate)
- Each session should have a minimum of two organizers and/or presenters. Based on feedback received from earlier years, please note that in general graduate students are not permitted to participate as instructors.
- A brief description of the organizers indicating the relevant qualifications to the proposal.
- Where appropriate, a brief description of the presenters indicating the relevant qualifications and teaching experience. Session attendees often consider the reputation and standing of the presenters as one of their criteria for choosing particular sessions.
- Session history
- Please indicate whether the session has been presented at another meeting previously.
- Promotional Session Description, up to 75 words
CLICK HERE to submit your proposal.
Proposal Evaluation
All submissions will be evaluated by a committee, which will consider the following criteria:
- Relevance, interest, and value of the topic to attendees
- Completeness, clarity, and quality of the proposal and materials
- Expertise and experience of the presenters in the proposed topic
- Expertise and experience of the organizers in delivering a successful educational experience
- Effectiveness of the proposed presentation approach
- If the session has been presented previously the participant evaluations will be considered
Session Materials
The presenters agree to provide participants with teaching materials that include:
- Copies of the slides in Powerpoint or PDF format for printing.
- Copies of relevant articles/book chapters published by the presenters may be provided as Supplementary Information. Presenters will have to obtain copyright permission from their publishers, as required.
Copyright
The authors will grant copyright to session materials to the ISCB for a period to extend from acceptance through August 1, 2019, and they agree that their materials may be made available for use in perpetuity through ISCB.
Compensation
Each session team will be provided:
Free registration for up to two team members presenting the tutorial and up to two (2) complimentary passes to the ISCB-Africa ASBCB conference. Unfortunately, travel funding is not available at this time.
Key Dates
| Tutorial Program Deadline | 28 June 2019 |
| Tutorial Program Acceptance Notification | 15 August 2019 |
| Tutorial Program Material | 1 November 2019 |
| Tutorial Program Dates | 14-15 November 2019 |
Travel Fellowships
We are raising funds to provide travel fellowships for African students to attend the ISCB Africa ASBCB 2019 Conference on Bioinformatics.
The Aim is to bring African students together to introduce them to a variety of research projects in computational biology, increase their awareness of the broad range of opportunities that exist in the field, and introduce them to some of the people leading this research internationally. The conference provides a great opportunity for students as it is preceded by bioinformatics workshops.
Funding and Eligibility
- Funding will support the registration, travel and accommodation of students. It will not cover visa fees, meals or subsistence.
- The applicant must be a current member of ISCB and/or ASBCB.
- Applicants need to have submitted a poster or paper for this conference; only accepted student poster and paper submitters will be eligible for funding, abstract submission deadline is Sept 13; poster submission deadline is Sept 30
- Notifications will occur on October 8th.
APPLICATION DEADLINE SEPT 15
SUBMIT APPLICATION HERE
Getting Here and Around
All International flights terminate at KOTOKA INTERNATIONAL AIRPORT in Accra, the Capital city of Ghana
From Accra to Kumasi transport by bus, it costs between USD 8.00 to USD10.00 with respect to mini buses, big and small Yutong Buses, STC coaches, and VIP buses. One can also travel from Accra international airport to Kumasi by air, 45 minutes flight with domestic airline such as AWA orPassionair. Taxis fare from Kumasi Airport to KNUST Campus is about $6:00 - $8:00.
For persons within and around the Kumasi Metropolis, the first access point to KNUST is Tech. Junction, a major station just outside the main gate of the University. From any point in and around the metropolis, one can board any vehicle, be it private or commercial to Tech Junction.
Getting to and around KNUST campus, which is about 16 km2 is an easy task for all. There arefree bus services. On arrival at Tech. Junction, which is a main transport terminal just outside the main gate of this prestigious University, one can locate several avenues to board a car to get to the Campus. First is by transport through any of our gates to campus in a private vehicle. Private vehicles are allowed into main KNUST campus without any restrictions.
The organizers can also arrange KNUST mini bus to transport delegates from Accra to Kumasi or internal travels in Kumasi in groups of any number.