| 11 | | == Technical == |
| | 13 | In general the project evaluated quite positive, if we had to rate ourselves we would give the project a 7. We identified several things that we feel we should try to keep and implement again in follow-up projects: |
| | 14 | |
| | 15 | * Weekly Skype calls; |
| | 16 | * Mailing list; |
| | 17 | * Open communication and low-threshold to find each other; |
| | 18 | * Sharing of best practices nationally and internationally; |
| | 19 | * Forming the group; |
| | 20 | * Access to international collaboration; |
| | 21 | * Sharing knowledge and code via wiki+svn; |
| | 22 | * Self-organization in working groups along sensible lines; |
| | 23 | * Using pragmatic solution and get started; |
| | 24 | * The involvement of NBIC !BioAssist was instrumental in establishing the group. |
| 14 | | === File management & replication === |
| 15 | | * General backup strategy and restore? |
| 16 | | * What is where (ToC of files)? |
| 17 | | * Is the file in hand the same as in ToC (checksum)? |
| 18 | | * What version is this file (e.g. multiple align runs) |
| 19 | | * Does the researcher have the file available on site? |
| 20 | | * Data freeze: can we mark data sets. |
| 21 | | * Data librarian: who is responsible for keeping the lists |
| | 27 | === Technical === |
| | 28 | ==== File management & replication ==== |
| | 29 | * General backup strategy and restore? |
| | 30 | * What is where (ToC of files)? |
| | 31 | * Is the file in hand the same as in ToC (checksum)? |
| | 32 | * What version is this file (e.g. multiple align runs) |
| | 33 | * Does the researcher have the file available on site? |
| | 34 | * Data freeze: can we mark data sets. |
| | 35 | * Data librarian: who is responsible for keeping the lists |
| 23 | | ==== Action items ==== |
| 24 | | |
| 25 | | |
| 26 | | |
| 27 | | |
| 28 | | |
| 29 | | |
| | 37 | ===== Action items ===== |
| | 38 | * create a series of user stories describing the practical issue we encountered during the project to share with SARA and BigGrid |
| | 39 | * Version individual files, not the whole set because to big (+index, etc) |
| | 40 | * Have overview of who wants what |
| | 41 | * Create small files we can release as a whole, e.g. SNP releases |
| | 42 | * Sort out backup strategy, what to keep, how to distribute over the resources and make it automated. |
| | 43 | * Make people responsible for data management. |
| 31 | | === Distribution of the analysis === |
| 32 | | * Where do you compute what? There was not a clear plan on the usage of the resources. |
| 33 | | |
| 34 | | * Currently we depend on LISA and UMCG clusters. |
| 35 | | |
| | 45 | ==== Distribution of the analysis ==== |
| | 46 | * Where do you compute what? There was not a clear planning on the usage of the resources, the simple queueing and per scheduling of resource usage caused some project to get into trouble. |
| | 47 | * Can we really distribute analyses over multiple sites |
| | 48 | * Currently we most work was done on LISA (Imputation/GWAS) and UMCG (SV/Alignment) clusters, only some indel calling was done on the Grid, could have done more on the Grid. |
| | 49 | * What pipelines do we want to distribute and why, and what are the barriers??? |
| 37 | | ==== Action items ==== |
| 38 | | * Reduce dependency on single resources: |
| 39 | | * Make pipelines distributed: deploy pipelines on multiple clusters |
| 40 | | * Make dependent executable available on other clusters |
| 41 | | * Make data available on other clusters |
| | 51 | ===== Action items ===== |
| | 52 | * Reduce dependency on single resources: |
| | 53 | * Make pipelines distributed: deploy pipelines on multiple clusters |
| | 54 | * Make dependent executable available on other clusters |
| | 55 | * Make data available on other clusters |
| | 56 | * This is taken up within RP2 and the eBioGrid project. |
| 51 | | == Organizational == |
| 52 | | * Coordination: Communication problems |
| 53 | | * Overview of external GoNL projects |
| 54 | | * Very good that we have a SC member (Cisca) on the call all the time. |
| 55 | | * Foreign contributors is nice, but it seems like they take away nice projects away. Need better communication. |
| 56 | | * Who is responsible for what? |
| 57 | | * Decentralized management (we can not boss other locations) |
| 58 | | * Organization: |
| 59 | | * It's not always clear which resources are actually available |
| 60 | | * SV team has too little man power to do the work (largely volunteers, hard to stimulare people) |
| 61 | | * Some groups could use some strengthening from one or more experienced people (Pheno, Imputation) |
| 62 | | * Not clear what should go into which paper, responsibility for the papers. |
| 63 | | ==== Action items ==== |
| 64 | | * Communication: |
| 65 | | * At every Steering Committee meeting have one of the subproject report results to Steering Committee |
| 66 | | * Organisation: |
| 67 | | * Ask the Steering Committee about available human resources (do the GoNL members get the time they need?) |
| 68 | | * Group responsible of rolling roadmap for one year (get from the steering committee) |
| 69 | | * Have more bioinformaticians in the steering committee and recognition of that |
| 70 | | * The technical people should get appreciation for their scientific contribution! |
| 71 | | * Need experienced person for each working group (SV is okay, imputation and pheno are a bit light because Yurii left) |
| 72 | | * Science / Roadmap: |
| 73 | | * Paper plan |
| 74 | | * Get from the steering committee general directions, very broad, what can / should do next with the data (GoNL flag, or just using) |
| | 66 | === Organizational === |
| | 67 | * Coordination: Communication problems |
| | 68 | * Overview of external GoNL projects |
| | 69 | * Very good that we have a SC member (Cisca) on the call all the time. |
| | 70 | * Foreign contributors is nice, but it seems like they take away nice projects away. Need better communication. |
| | 71 | * Who is responsible for what? |
| | 72 | * Decentralized management (we can not boss other locations) |
| | 73 | * It's not always clear who is paid by the project and who is a volunteer, you can only kindly ask the volunteers to do tasks. |
| | 74 | * It was approached as a scientific project, which meant there was not always a clear direction from above. |
| | 75 | * Organization: |
| | 76 | * It's not always clear which people resources are actually available |
| | 77 | * SV team has too little man power to do the work (largely volunteers, hard to stimulare people) |
| | 78 | * Some groups could use some strengthening from one or more experienced people (Pheno, Imputation) |
| | 79 | * Not clear what should go into which paper, responsibility for the papers. |
| 76 | | ==== Things to Keep ==== |
| 77 | | * Weekly skypes |
| 78 | | * Mailing list |
| 79 | | * Open communication and low-threshold to find each other |
| 80 | | * Sharing of best practices nationally and internationally |
| 81 | | * Forming the group |
| 82 | | * Access to international collaboration |
| 83 | | * Sharing knowledge and code via wiki+svn |
| 84 | | * Self-organization in working groups along sensible lines |
| 85 | | * Using pragmatic solution and get started |
| | 81 | ===== Action items ===== |
| | 82 | * Communication: |
| | 83 | * At every Steering Committee meeting have one of the subproject report results to Steering Committee |
| | 84 | * Organisation: |
| | 85 | * Ask the Steering Committee about available human resources (do the GoNL members get the time they need?) |
| | 86 | * Group responsible of rolling roadmap for one year (get from the steering committee) |
| | 87 | * Have more bioinformaticians in the steering committee and recognition of that |
| | 88 | * The technical people should get appreciation for their scientific contribution! |
| | 89 | * Need experienced person for each working group (SV is okay, imputation and pheno are a bit light because Yurii left) |
| | 90 | * Science / Roadmap: |
| | 91 | * Paper plan |
| | 92 | * Get from the steering committee general directions, very broad, what can / should do next with the data (GoNL flag, or just using) |
