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<申請公告>2018 美國一年研究實習計畫甄選(NAL)

活動專區
張貼人:李依芸公告日期:2018-01-03

 2018美國一年研究實習研究生甄選(NAL)

1-year internship in U.S. (NAL)

Ø   申請資格:臺大電資院碩、博士班研究生

名額:2-5

實習期間:一年 (約自20188月起)

Who: 2-5 Ms and Phd students in College of Electrical Engineering and Computer Science, NTU

Internship period: 1 year (approximately starting from Aug. 2018)

**薪資及福利Salary and benefits

1.            年薪25,000美金 25000 USD annual salary

2.            臺美往返機票,補助上限為每位學生4,000美金

Flight tickets between Taiwan and U.S. under maximum 4000USD per student

3.            搬家津貼settling in allowance: $1,000 (USD)

4.            美國健康保險補助 US health insurance

l   2018United States Department Of Agriculture美國農業部國家農業研究局(USDA-ARS)與我院合作之研究實習計畫徵選碩博士生參與!實習單位為美國農業部國家農業圖書館 (National Agricultural Library, NAL) 網頁連結請見:www.nal.usda.gov

2018 internship at National Agricultural Library (NAL), United States Department Of Agriculture. More info about NAL at www.nal.usda.gov.

Ø   申請審查時程Application Timeline

1.          申請截止日期:2018129 Application Deadline: Jan 29, 2018

2.          NAL最終錄取結果公告:2018227

NAL Announce acceptance: Feb 27, 2018

3.          學生確認接受截止日期:201832

Acceptance deadline for students: Mar 2,2018

4.          簽證申請:20183月起 Visa application: since Mar, 2018

5.          出發前往美國:201886Departure to US: August 6th, 2018

(申請簽證相關時程為預估,請注意個人學業生涯規劃)

Ø   應繳交之中文審查資料如下:2018NAL申請書 version20180104

Ø   應繳交之英文審查資料如下:

1.     Undergraduate and postgraduate official transcripts (GPA)

2.     Statement of Interest

3.     2 reference letters

4.     Papers (journal or conference) or sample examples of programming skills

5.     English Language Certificate

l   Application documents:

1.          2018NAL申請書Application form version20180104

2.          Undergraduate and postgraduate official transcripts (GPA)

3.          Statement of Interest

4.          2 reference letters

5.          Papers (journal or conference) or sample examples of programming skills

6.          English Language Certificate

*若無英語能力檢定成績,依然可提申請;若獲NAL錄取,需於辦理簽證前補交檢定證明。

*若英語能力經NAL檢定後認定須加強,學生可獲NAL補助,並於出國前完成要求之英文課程。

* English Language Certificate can be provided after NAL acceptance before visa application. If NAL consider further improvement in English proficiency necessary, the NAL-accepted student needs to complete required English courses before departure to US.

申請書,交換心得,申請資訊下載Download the application document and more info

https://www.space.ntu.edu.tw/navigate/s/9C700CCB2B424BD19AB965757BCECA3EQQY

本計畫收件截止日期為201812917:00,有意願之申請者請於收件截止日前,將申請書連同所有資料交至博理館二樓202室尹子真小姐,由電資學院統一審查後再將決定之推薦名單送至NAL

Please submit all application documents to Mrs. Dana Yiin @ room 202 in Barry Lam Hall before 17:00 on Jan 29. The college of EECS will review all applicants and make nomination to NAL.

 

 

For Internship Announcement

The Insect 5,000 Genome initiative (i5K) is an international collaboration to sequence the genomes of 5,000 arthropods important to food safety, agriculture, and human health.  Interns will work closely with the National Agricultural Library’s (NAL) bioinformatics team to build tools and services for the i5k Workspace@NAL (https://i5k.nal.usda.gov; doi: 10.1093/nar/gku983; https://github.com/NAL-i5K). The i5k Workspace is a web resource providing dissemination, visualization, and curation tools for ‘orphaned’ insect or arthropod genome projects. This is an actively growing project, and there are many possible development opportunities. Projects focus on application/tool development and biocuration services for our research community.

Our team is seeking individuals with experience in bioinformatics and/or or tool and application development to join our team at the NAL for one year. 

Desired Skills and Related Experience

Exact skills, knowledge and experience will vary based on the projects selected. The list below contains desired, but not required skills. 

·         Bioinformatics

o    Gene prediction and functional annotation

o    Comparative genomic analysis

o    Biocuration

o    Unix command line (including usage of high-performance computing systems)

·         Data visualization

o    Google APIs and SDKs (Analytics, Charts, Maps)

o    Other JavaScript libraries (such as Flot/jQuery, D3.js, Processing.js, etc.)

o    User experience/ User interface

·         Programming languages

o    Object oriented programming (Java, Python)

o    Dynamic scripting languages (Perl, PHP)

o    Statistical programming (R)

·         Database design and programming

o    Entity-relation modeling and normalization

o    Performance tuning

o    Data warehouses, business intelligence, and data mining

·         Open source software

o    LAMP (Linux/Apache/MySQL/PHP or Python ,etc.) software stack

o    Web framework (Django, Google Web Toolkit)

o    Middleware (JBoss, Tomcat)

o    Content management (Drupal)

o    Version control (Git, Github/GitLab)

o    Continuous integration (Travis, Jenkins CI)

Potential Opportunities

Interns also have the opportunity to develop their own project ideas related to the i5k Workspace.

Informatics Projects

1.Develop a workflow to migrate submitted genomic data to a repository system (e.g iRods, git-annex, or other)     

a.Design a system to migrate i5K genome data with associated metadata;     

b.Develop rules to automate data ingestion and synchronization;     

c.Implement the system, locally;      

d.Develop rules for sharing with external resources     

                                                  i.      CyVerse

                                                ii.      AgDataCommons

                                              iii.      Other systems with clearly defined APIs for access?

2.Build new Web services for the i5K Workspace (such as InterMine / http://intermine.org/ ). This is an on-going project assessing user needs and building solutions for their pain points.     

a.Assess user needs for bioanalytical tools and services;     

b.Identify potential solutions;     

c.Assess feasibility for integration into the i5K Workspace;      

d.Extend existing services to provide new functionality;     

e.Build and incorporate tools/solutions into the i5K Workspace.      

3.Find, modify, or build community interaction tools.  The student will interact with i5k Workspace users to assess common needs.     

a.Search for third party solutions for common needs;     

b.Test and modify third party solutions when needed; or      

c.Build new tools if needed.      

4.      Apollo development. Enhancement of the program for i5k needs. Interaction with Apollo group (http://genomearchitect.github.io/).

5.Develop tools and integrate data to support comparative analyses of arthropod genomic data. Homology data are available for many i5k species. This information can be added to gene pages, visualized in browsers, and represented in many other ways to support comparative analysis.     

6.Develop improved analytics and metrics. Build systems and tools to display our system resources more clearly: Examples may include current data types with numbers (e.g. 50 RNAseq tracks, 20 gene predictions, 1 OGS) displayed by organism or globally. For internal record-keeping, track number of registered users globally or by organism, current status of project (e.g. actively annotating, building OGS, no current annotation).      

7.Develop the visualization of organisms included in the i5k Workspace as a taxonomic tree.     

Bioinformatics Projects

1.Develop a gene prediction pipeline tuned towards specific gene families. Most genome annotation pipelines predict certain gene families poorly. This project would 1) identify genes and gene families that are important for arthropod researchers and are typically poorly predicted and 2) develop methods to improve annotation accuracy.      

2.Investigate and implement new ways for i5k Workspace users to compare datasets. Many i5k Workspace users are interested in comparative genomics. We would like to explore and identify new ways to visualize and analyze our datasets that would provide our users other ways to interact with datasets that would facilitate comparative genomics insights.     

3.Identify or develop and apply methods to measure annotation accuracy. Annotations are rarely perfect. To improve our assessments of annotation quality – of both automated and manually curated annotations – we would like to explore and implement methods that evaluate annotation accuracy.     

4.Biocuration. The i5k Workspace enables manual curation of gene models by the i5k community. We are seeking an intern interested in manual curation and biocuration to: identify workflows for new annotators; create manual curation tutorials; and interact with the i5k manual curation community to identify curation needs.     

Examples of past and current projects:

·         Development of a novel BLAST user-interface (https://github.com/hotdogee/django-blast)

·         Development of a single-sign on system to the i5k Workspace using Django

·         Programs to check the quality of the GFF3 format (https://github.com/hotdogee/gff3-py)

·         Program to compare two GFF3 files (https://github.com/chienyuehlee/gff-cmp-cat)

·         A ‘toolkit’ for the GFF3 annotation format, including programs to QC and merge two gff3 files for Official Gene Set generation (https://github.com/NAL-i5K/GFF3toolkit/)

·         Implementation of HMMER and ClustalW web services (https://github.com/NAL-i5K/genomics-workspace)

·         Application stress testing (our internal tests were incorporated into the Apollo codebase)

·         A program to convert several file types between assembly coordinate systems: https://github.com/NAL-i5K/coordinates_conversion 

Publications of past interns

·         Panfilio, K.A., et al. 2017. Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome. bioRxiv 201731; doi: 10.1101/201731. Interns Mei-Ju May Chen and Chien-Yueh Lee are co-authors.

·         Schoville, S., et al. 2017. A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae). bioRxiv, doi: 10.1101/192641. Accepted, Scientific Reports. Intern Mei-Ju May Chen is a co-author.

·         Chen, M.-J. M., Lin, H., Chiang, L., Childers, C.P., and Poelchau, M.F. Methods in Molecular Biology. Accepted. The GFF3toolkit – QC and Merge Pipeline for Genome Annotation. Interns Mei-Ju May Chen, Yu-Yu Lin and Li-Mei Chiang are co-authors.

·         Poelchau, M.F., Chen, M.-J. M., Lin, Y.-Y., and Childers, C.P. Methods in Molecular Biology. Navigating the i5k Workspace@NAL – a resource for arthropod genomes. Accepted. Interns Mei-Ju May Chen and Yu-Yu Lin are co-authors.

·         Saha, S., et al. (2017). Improved annotation of the insect vector of Citrus greening disease: Biocuration by a diverse genomics community. Database, bax032, https://doi.org/10.1093/database/bax032. Intern Mei-Ju May Chen is a co-author.

·         Benoit, J.B., et al. (2016). Unique features of a global human ectoparasite identified through sequencing of the bed bug genome. Nat Commun 7. Interns Chien-Yueh Lee and Han Lin are co-authors.

·         McKenna, D.D., et al. (2016). Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle–plant interface. Genome Biol. 17, 227. Interns Chien-Yueh Lee and Han Lin are co-authors.

·         Poelchau, M., et. al. (2014). The i5k Workspace@NAL--enabling genomic data access, visualization and curation of arthropod genomes. Nucleic Acids Res. (43), D714-D719. Interns Chien-Yueh Lee, Han Lin and Jun-Wei Lin are co-authors.

計畫承辦人:尹子真 02-33661566 

yiintc8@ntu.edu.tw

博理館202辦公室
最後修改時間:2018-01-04 AM 9:19

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