Bachelor’s/ Master’s Theses and Internships in Digital Engineering: Design and implementation of generic RESTful-APIs for omics databases

Background:
The IPK hosts dozens of databases that manage millions of data points and cover terabytes of omics data from the last seven decades of plant research. High-throughput omics technologies produce genomics, phenomics, environmental and metabolomics data on a large scale. In this context, the research group “Bioinformatics and Information Technology” (BIT) is contributing towards the evolution of the IPK into a digital resource center which shares digital plant genetic resources as well as the developed technologies and services within the international research community.

Your tasks:
The thematic frame for theses is the design and implementaion of RESTful services that open institutional databases to provide self-describing data access. A reference implementation should be realized in a JVM-based programming language, preferably Java or Groovy. The use case focuses on API-level access as well as containerized export of genotyping and phenotyping datasets using the ISA concept. ISA is a generic concept to provide domain independend and self-describing data exchange of investigations (project context), studies (unit of research) and assays (measurement) of data entities. It supports data serialization as TSV files, JSON or RDF.

You fit to us:
• You are interested in contributing to this emerging field of data science and bioinformatics and would like to work on your bachlor’s or master’s thesis within the BIT research group.
• You are highly motivated and communicative and would like to improve your skills in enterprise-level software development and bioinformatics

We offer you:
• A cutting-edge, innovative research environment and a state-of-the-art IT infrastructure, comprising cloud-computing capacities, a HPC-ready server, enterprise-level database management, storage and web server infrastructure
• Compensation as a student research assistant for a max. of 6 months
• Housing near to the campus (subject to a fee and upon request)

If you need further information, feel free to contact Mr. Daniel Arend (arendd@ipk-gatersleben.de) Tel.: +49 (0)39482 5842.


What you need to know:
For us, your qualifications and strengths count. Therefore, everyone – independent from gender, origin, age, or possible disability – is welcome. The IPK is striving to increase the proportion of women in sectors where they are underrepresented and therefore explicitly encourages qualified women to apply. As an institution which has been awarded the Certificate for Career and Family (“berufundfamilie”), we offer family-friendly working conditions and flexible working hours. The IPK has set a goal to employ more people with disabilities. Qualified applicants with a disability will be given preference.


Your application:
We look forward to receiving your online application (http://www.ipk-gatersleben.de/en/job-offers/). If you have questions or require more information, please contact Ms. Jacobi (jobs@ipk-gatersleben.de) and indicate the reference number 26/03/18 in your correspondence.

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Postdoctoral Researcher in the Field of Plant Meiosis (f/m)

The independent research group Meiosis is interested in the process of plant meiosis that generates genetic variation through homologous recombination. To support our team, we are looking for a highly motivated postdoctoral candidate.


Your tasks:
• You will be responsible, as a member of a team, for executing studies focused on the identification and functional analysis of posttranslational modifications of meiotic chromosome axis and synaptonemal complex proteins in Arabidopsis and barley.
• You will perform molecular cloning and plant transformations using biochemical and cytological methods.
• You will communicate with cooperation partners.
• You will present results at scientific meetings and write journal articles.

Your qualifications and skills:
• You are completing or have obtained a Ph.D. degree in the field of molecular biology, cell biology, biochemistry, or a related discipline.
• You have a strong publication record.
• You have experience with plant models, molecular and cell biological techniques and/or biochemistry.
• Experience in the field(s) of meiosis and/or posttranslational protein modifications is highly desirable but not required. In general, quality of past research is more important than experience in a specific field.
• You possess solid English skills.

You fit to us:
• You are fascinated by plant biology and a highly-motivated person with team spirit.
• You want to build a career in science and you have a strong drive to succeed.
• You can organize your work independently.
• You have previously demonstrated the capacity to master the broad skill set necessary for the successful completion of a research project.
• You want to become a member of a young and dynamic team.

We offer you:
• The opportunity to work in a world-class research centre with state-of-the-art facilities and scientists from all over the world
• A friendly and productive working atmosphere
• A project-based position within an ERA-CAPS consortium, offering excellent scientific collaborations and providing a unique opportunity to deepen and broaden your research profile and advance your independent academic career
• A position, starting July 1st, 2018 or later, limited for 36 months
• A gross salary up to 100 % E13 TV-L

If you need further information please contact Dr. Stefan Heckmann (heckmann@ipk-gatersleben.de; +49 (0)39482 5608.

What you need to know:
For us, your qualifications and strengths count. Therefore, everyone – independent from gender, origin, age, or possible disability – is welcome. The IPK is striving to increase the proportion of women in sectors where they are underrepresented and thus explicitly encourages qualified women to apply. As an institution which has been awarded the Certificate for Career and Family (“berufundfamilie”), we offer family-friendly working conditions and flexible working hours. The IPK has set a goal to employ more people with disabilities. Qualified applicants with a disability are given preference.

Your application:
We are looking forward to receiving your online application (http://www.ipk-gatersleben.de/en/job-offers) until May 27th, 2018. If you have questions or require more information, please contact Ms. Jacobi (jobs@ipk-gatersleben.de). Please indicate the reference number 25/03/18 in your correspondence.

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Postdoctoral Researcher in Plant Cell Biology (Registration Number 7/2018)

A postdoctoral position is available in the laboratory of Prof. Alain Tissier at the Leibniz Institute of Plant Biochemistry in Halle Germany. The position is for an EU-funded project on chicory (for more information on this project see: http://chicproject.eu/). The tasks of the successful candidate will be to generate transcriptome data concerning laticifer development in chicory. For this position expertise in plant cell biology is a must. Additional experience in molecular biology and analysis of RNA-Seq data is a plus.

Academic requirements: PhD.

The position is a replacement due to a maternity leave and is for one year starting June 1st, 2018.  

The Leibniz Institute of Plant Biochemistry is a governmental research institute located on the Weinberg Campus of the Martin Luther University Halle-Wittenberg. The institute offers

  • essential infrastructure from the existing programs in stress and developmental biology (Dierk Scheel), molecular signal processing (Steffen Abel), bioorganic chemistry (Ludger Wessjohann), and cell and metabolic biology (Alain Tissier),
  • state of the art technology for analytical, synthetic and structural chemistry, proteomics, metabolic profiling, biochemistry and molecular and cell biology,
  • an energetic working environment with a multidisciplinary approach to natural product, molecular interaction, plant microbe interaction and gene function analyses.

Appointments will be made according to TV-L, E 13 for 1 year starting June 1st, 2018. Applicants with appropriate expertise and a proven publication record should submit their CV and publication list stating registration number 7/2018, together with a short sketch of their research interests, and the names of two academic referees in a single pdf document to

Leibniz Institute of Plant Biochemistry

AG Personal

Kerstin Balkenhohl

Weinberg 3

D-06120 Halle or

bewerbungen@ipb-halle.de

The Leibniz Institute of Plant Biochemistry is an affirmative action employer. Further information can be found under http://www.ipb-halle.de or obtained by contacting Alain Tissier (email: atissier@ipb-halle.de, phone: +49-345-5582-1500).

Closing date for applications is April 15th, 2018.

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Postdoctoral Research Associate

The Leibniz Institute of Plant Biochemistry (IPB) is an international research institute located on the weinberg-campus of the Martin Luther University Halle-Wittenberg, Halle, Germany (www.ipb-halle.de). The IPB is a member of the Leibniz Association and a foundation under public law. The IPB-Department of Molecular Signal Processing invites applications to fill the position of Postdoctoral Research Associate.

Candidates must hold a PhD degree and should have thorough research training and relevant experience in one of the following areas: plant molecular biology/genetics, plant cell biology/physiology or protein biochemistry/structural biology. Applicants should be curious and creative and possess excellent analytical as well as communication skills, including fluency in English. The successful candidate will conduct and develop research in the field of either nutrient sensing, hormone action, or calcium signaling, depending on interest and expertise.

The appointment will be for three years. Salary and social/health benefits will be based on German law (public employees, TV-L E13). Please, contact Prof. Steffen Abel for additional information (sabel@ipb-halle.de; Phone: 0049 (0) 345 5582 1200).

Applications must include a cover letter describing research accomplishments and interests, a CV plus publication list, and contact details of 2-3 referees. Please, email a single pdf document quoting reference number 5/2018 to bewerbungen@ipb-halle.de. Review of applications will start immediately and continue until the position is filled. 

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Postdoctoral Researcher tomato transformation

A postdoctoral position is available in the laboratory of Dr. Sylvestre Marillonnet at the Leibniz Institute of Plant Biochemistry in Halle, Germany. In the frame of a BMBF-funded project to increase the frequency of gene replacement in plants, techniques to improve tomato transformation and regeneration using tissue culture will be developed. The project will require cloning and transient expression of transcription factors involved in plant development. The successful candidates must have a Ph.D. and a strong record of accomplishment in plant molecular biology. Previous experience with plant tissue culture will also be useful. The starting date of this 2-year position is July 1st, 2018.

The Leibniz Institute of Plant Biochemistry is a governmental research institute located on the Weinberg Campus of the Martin Luther University Halle-Wittenberg. The institute offers

  • essential infrastructure from the existing programs in stress and developmental biology (Dierk Scheel), molecular signal processing (Steffen Abel), bioorganic chemistry (Ludger Wessjohann), and cell and metabolic biology (Alain Tissier),
  • state of the art technology for analytical, synthetic and structural chemistry, proteomics, metabolic profiling, biochemistry and molecular and cell biology,
  • an energetic working environment with a multidisciplinary approach to natural product, molecular interaction, plant microbe interaction and gene function analyses.

The Leibniz Institute of Plant Biochemistry is an affirmative action employer. Payment is according to local regulations TV-L.

Further information can be found under http://www.ipb-halle.de or obtained by contacting Sylvestre Marillonnet (email: smarillo@ipb-halle.de, phone: +49-345-5582-1536).

 

Applicants with appropriate expertise and a proven publication record should submit their CV and publication list stating registration number 4/2018, together with a short sketch of their research interests, and the names of two academic referees as a single pdf document to bewerbungen@ipb-halle.de

Closing date for applications is 15.04.2018.

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Postdoctoral Researcher (Postdoc) in Developmental Genetics of Cereal Crops (f/m)

The culturally diverse, independent HEISENBERG-Research Group “Plant Architecture” is primarily interested in basic research questions concerning how cereal inflorescences, called spikes, develop and how this contributes to yield formation.


Your tasks:
• Work in a research team to elucidate the molecular mechanisms of spikelet/floret development and spike architecture using the latest genetic, physiological and metabolic approaches in the temperate model crop barley
• Discover, isolate and functionally characterize QTL or genes for spike/spikelet/floret traits in barley
• Use microscopic precision phenotyping of captured images, image analysis and field evaluations for trait quantification and patterning
• Handle NGS datasets for RNA-Seq or SNP detection and linkage analysis using R


Your qualifications and skills:
• You have a PhD or equivalentdegree in biology, agriculture or any related field.
• You have a proven track record and extensive experience with genetic analyses (e.g., Linkage, QTL and GWAS analyses); hands-on experience in phenotyping plants (e.g., cereals) is amust. Experience with molecular, cytological and/or biochemical techniques or R programming is desirable.
• You like microscopy.
• You possess the solid English skills which are necessary to work in our multicultural environment.

You fit to us:
• You are a highly motivated person.
• You can organize your work independently.
• You have previously demonstrated the capacity to master the broad skill set necessary for the successful completion of a research project.
• You can guide and mentor less experienced team members.
• You are a team player.

We offer you:
• The opportunity to work in a world-class research centre with state-of-the-art facilities and scientists from all over the world
• A friendly and productive working atmosphere
• An employment, starting as early as July 1st, 2018, limited for 24 months with the possibility of an 18-month extension (total: ~3.5 years) upon positive evaluation
• Gross salary will be up to 100% E13 TV-L

For further information, please contact PD Dr. Thorsten Schnurbusch (schnurbusch@ipk-gatersleben.de).

What you need to know:
For us, your qualifications and strengths count. Therefore, everyone – independent from gender, origin, age, or possible disability – is welcome. The IPK is striving to increase the proportion of women in sectors where they are underrepresented and therefore explicitly encourages qualified women to apply. As an institution which has been awarded the Certificate for Career and Family (“berufundfamilie”), we offer family-friendly working conditions and flexible working hours. The IPK has set a goal to employ more people with disabilities. Qualified applicants with a disability will be given preference.

Your application:
We are looking forward to receiving your online application (http://www.ipk-gatersleben.de/en/job-offers) until April 1st, 2018. If you have questions or require more information, please contact Mrs Jacobi (jobs@ipk-gatersleben.de). Please indicate the reference number 18/02/18 in your correspondence.

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Independent Junior Research Group Leader

The Leibniz Institute of Plant Biochemistry (IPB) at Halle (Saale), Germany, invites applications to fill the position of Independent Junior Research Group Leader. Candidates with international postdoctoral experience will have to demonstrate their potential to develop a vigorous and competitive research program on important problems in plant biology/chemistry at the molecular, biochemical or systems level.

The IPB is an international research institute of about 200 employees and located on the weinberg-campus of the Martin Luther University Halle-Wittenberg. Its research theme focuses on the chemical diversity, metabolism, molecular action, and biological roles of plant and fungal natural products, with an emphasis on specialized metabolites, signaling molecules, and underlying regulatory networks. The IPB provides excellent research facilities and offers a stimulating academic environment fostering multidisciplinary approaches to the analysis of gene and protein function, structure and activity of natural products, biomolecular and organismic interactions, as well as state-of-the-art technologies for organic chemistry and biochemistry, molecular and cell biology, metabolic profiling and proteomics. Additional information is available at http://www.ipb-halle.de.

The appointment will be initially for 3 years with the possibility of a 3-year extension upon positive mid-term evaluation. Compensation will be according to TV-L, E14 or E15, depending on prior professional experience. The IPB provides equipped laboratory space, annual funds for consumables, and salaries for one postdoctoral researcher and one technical assistant. The successful candidate will be expected to establish a dynamic and growing research group by attracting extramural funds. The IPB will host and provide additional funds to outstanding young researchers who have been awarded a stipend or grant by external agencies.

Applicants with a strong record of high-quality publications in reputed journals should submit a letter describing their research accomplishments and future research interests (no more than 5 pages), Curriculum Vitae, publication list, and contacts of 3 references. Please send your applications quoting reference number 3/2018 as a single pdf document to bewerbungen@ipb-halle.de.

For further information, please contact Prof. Dr. Steffen Abel (steffen.abel@ipb-halle.de).

The IPB is an equal opportunity employer and promotes a family-friendly working environment.

Closing date for applications is 16. 04. 2018.

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PhD Student of Chromosome Biology (f/m)

The research group Chromosome Structure and Function studies chromosomes in interphase nuclei and dividing cells of model plants and cereal crops like Arabidopsis and barley, respectively, to understand the organization and function of chromatin during the cell cycle.


Your tasks:
• You will study three-dimensional organization of chromatin across the cell cycle using chromosome conformation capture sequencing and super-resolution microscopy
• You will prepare oligo-FISH probes to analyse the 3D organization of chromatin in interphase nuclei and metaphase chromosomes at the nanoscopic level.
• You will work in a German-Czech project together with specialists of flow-cytometry, Hi-C techniques, and bioinformatics.
• Your will present your results in scientific articles and at international conferences.


Your qualifications and skills:
• You have a master’s degree in molecular biology, biochemistry, or related fields.
• You possess knowledge of molecular, cytological and/or biochemical techniques. Experience working with plants (e.g., cereals, barley) is desired.
• You have a strong molecular-cytogenetic background.
• You have solid English skills, which is a prerequisite for effective work in our multicultural environment.

You fit to us:
• If you are a bright, highly motivated and enthusiastic person.
• If you are interested in chromosome research and microscopy and see your future in academic research.
• You have the ability to work independently, as well as part of a team.

We offer you:
• The opportunity to work in a modern research centre with state-of-the-art facilities.
• An interdisciplinary research environment at the intersection of life sciences, bioinformatics, and microscopy/nanoscopy.
• A project-based position limited to 36 months.
• A gross salary of 65% of up to E-13 TVL.

If you need further information, feel free to contact PD Dr. Veit Schubert (schubertv@ipk-gatersleben.de).

What you need to know:
For us, your qualifications and strengths count. Therefore, everyone – independent from gender, origin, age, or possible disability – is welcome. The IPK is striving to increase the proportion of women in sectors where they are underrepresented and therefore explicitly encourages qualified women to apply. As an institution which has been awarded the Certificate for Career and Family (“berufundfamilie”), we offer family-friendly working conditions and flexible working hours. The IPK has set a goal to employ more people with disabilities. Qualified applicants with a disability will be given preference.

Your application:
We are looking forward to receive your online-application (http://www.ipk-gatersleben.de/en/job-offers/).
If you have questions or require more information, please do contact Ms. Jacobi (jobs@ipk-gatersleben.de). Please indicate the reference number 06/01/18 in your correspondence

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Scientist (PhD Student) in Image Analysis

The Image Analysis group of the Molecular Genetics department at IPK Gatersleben deals with the development of computational methods for derivation of quantitative traits of crop plants from multimodal and multidimensional image data acquired in high-throughput with multispectral 2D and 3D camera systems. To support our team, we are currently looking for a qualified researcher (PhD Student).


Your tasks:
• You will develop software solutions for processing and analysis of multimodal and multidimensional image data from high-throughput plant phenotyping experiments such as time-series of multispectral 2D and 3D images.
• You will communicate with internal and external cooperation partners.
• You will present results at scientific meetings and write journal articles.

Your qualifications and skills:
• You have a degree in informatics, mathematics, physics or similar educational background.
• You have good programming skills in one or more scientific programming languages (i.e., Matlab/Octave, Java, C/C++, Phyton, shell).
• You have experience working with signal/image processing, computer vision, spatial-temporal modeling and/or machine learning applications.
• Previous experience in plant image analysis or modelling is a plus.

You fit to us:
• You are a passionate software developer.
• You like to work in a team and to reach goals together.
• You like to work in an interdisciplinary environment on the boundary between computer and biological sciences.

We offer you:
• A cutting edge interdisciplinary research environment.
• Collegial working atmosphere.
• An employment limited for 36months.
• Gross salary will be up to E13 TV-L.

If you need further information, feel free to contact Dr. Evgeny Gladilin (gladilin@ipk-gatersleben.de).

What you need to know:
For us, your qualifications and strengths count. Therefore, everyone – independent from gender, origin, age, or possible disability – is welcome. The IPK is striving to increase the proportion of women in sectors where they are underrepresented and therefore explicitly encourages qualified women to apply. As an institution which has been awarded the Certificate for Career and Family (“berufundfamilie”), we offer family-friendly working conditions and flexible working hours. The IPK has set a goal to employ more people with disabilities. Qualified applicants with a disability will be given preference.

Your application:
We are looking forward to receive your online-application (http://www.ipk-gatersleben.de/en/job-offers/).
If you have questions or require more information, please do contact Ms. Jacobi (jobs@ipk-gatersleben.de). Please indicate the reference number 64/12/17 in your correspondence.

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